The Tyndale New Testament Commentaries Volume IV on John (Colin G Kruse) also notes that early readers may have understood it to be a polemic against Domitian who demanded that people worship him as Lord and God. This makes sense, Thomas’ confession acts as a theological climax to both John’s narrative and christological project. It is not only the final confession, it is an explicit reference to the themes which the author(s) have attempted to convey throughout the Gospel, which Francis J. Maloney contend are thus: “the narrator’s teaching on the logos in 1:1-2, Jesus’s unique use of the absolute ego eimi…and his claim ‘I and the Father are one’ (10:30…)” (Maloney, 537).

Raymond E. Brown in his Introduction to New Testament Christology (1994), actually lists this verse as one of the only three “passages where Jesus is clearly called God”, (along with Hebrews 1:8-9 and John 1:1). His argument on the matter is short, so to directly quote him on it:
“John 20:28: On the Sunday evening one week after Easter Jesus appears to Thomas and the other disciples, causing Thomas to confess him as “My Lord and my God.” This is the clearest example in the NT of the use of “God” for Jesus. Here Jesus is addressed as “God” (a nominative form with definite article, which functions as a vocative). The scene is designed to serve as a climax to the Gospel: As the resurrected Jesus stands before the disciples, one of their number at last gives expression to an adequate faith in Jesus. He does this by applying to Jesus the Greek (Septuagint) equivalent of two terms applied to the God of the OT (kyrios, “Lord,” rendering YHWH; and theos, “God,” rendering ‘Elohim). The best example of the OT usage is in Ps 35:23, where the psalmist cries out: “My God and my Lord.” It may well be that the Christian use of such a confessional formula was catalyzed by the Roman emperor Domitian’s claim to the title “Lord and God” (dominus et deus noster).” (p.188-189).
Additionally, a footnote in this section has Brown claim the idea that Thomas is separately addressing the Father had few proponents at the time of writing. This can be backed up with some other scholar’s opinions regarding Johannine Christology:
“Finally, on the association between the titles ‘Son of God’ and ‘God’ (cf 5.18). The argument of John 10.31-8 may certainly be said to reflect the older link between divine sonship and divinity and the ambivalence in their application to kings in ancient Israel (see above pp. 15, 17). But the argument of that passage is of the ‘how much more’ variety – if the law calls kings or judges ‘gods’ (Ps. 82.6), how much more is the one ‘whom the Father consecrated and sent into the world’ worthy of the tide? And elsewhere in the Johannine writings there is no question of the tide being used in a reduced sense. Not only the pre-existent Logos is god (1.1 – see below p. 241), but also the incarnate Son (1.18), as well as the risen ascended Christ (20.28).” (James D.G. Dunn, Christology in the Making, 1989, p.58).

“Another extremely noteworthy development seen in John 10 is the defence of Jesus not only bearing the authority of God but even being called ‘God.’ The Fourth Evangelist clearly does apply the designation ‘God’ to the risen Jesus in 20.28 (and perhaps in 1.18), but nonetheless shows a great reticence which his predecessors shared, to such an extent that it is not clear whether they intended to refer to Jesus as ‘God’ at all. In the period after John we notice a remarkable change: in Ignatius we already and a tendency to speak much more freely of Jesus as ‘God,’ and in later times even the Jewish-Christian Pseudo-Clementine literature defends this practice. This is very likely a result of the fact that in John we and a scriptural support and basis being provided for this Christian practice of calling Jesus ‘God.’ Thus, in spite of his own restraint and reticence in referring to the human being Jesus as ‘God,’ by providing an argument which sought to demonstrate the legitimacy of using this language in reference to Jesus, the Evangelist apparently encouraged its wider usage, and this usage helped shape the course which later christological development followed and the conclusions which it reached. And so we see in John 10, as in the other passages we have considered thus far, evidence of the role legitimation played in the development of Johannine Christology.” (James F. McGrath, John’s Apologetic Christology, 2001, p.130).

“At the entrance of Domitian’s temple in Ephesus stands a monument to the goddess Nike (meaning “victory”), celebrating the emperor’s victory over subjugated peoples. Where emperor worship had not previously been a widespread practice since the days of Caesar Augustus (19 b.c.e.–14 c.e.), Domitian reinstated it as a means of bolstering imperial power and loyalty. He even required his own lieutenants to regard him as “lord and god,” which suggests that the confession of Thomas, “My lord and my God!” (John 20:28), conveys a decisively anti-imperial thrust. Indeed, the last verse of 1 John (5:21) admonishes believers to “stay away from idols” as a more pointed injunction to “love not the world.” It would have been a direct statement against offering sacrifices to Caesar (either incense or a more substantive animal or grain offering), but it would also have challenged participation in civic festivals, which sometimes went on for days at a time.” (Paul N. Anderson, The Riddles of the Fourth Gospel, 2011, p.136)
Considering all of this, I’d say it’s likely that Thomas was referring to Jesus in John 20:28, as it would likely have been in reference to Domitian’s claim to the same title of “Lord and God”. That, of course, doesn’t mean your observation isn’t warranted. Taken at face value, it does seem to conflict with the Christology of other passages in John’s gospel. For instance Raymond E. Brown lists John 14:8 and 17:3 as “passages that seem to imply that the title of ‘God’ was not used for Jesus”, (p.175-176).

This can probably traced down to two separate ideas. First, the unity or disunity of the gospel as a whole. Anderson in The Riddles of the Fourth Gospel, goes over the idea that the gospel of John has multiple layers to it, and that it was extensively edited around 20 years after its initial composition by a separate author, citing the 21st chapter as an example since it seems as though the gospel was meant to end at John 20:31. There’s a chance that the later editor may have caused apparent conflicts within the theology.

Additionally, there’s also the explanation that the author generally felt it was appropriate to both refer to Jesus as God in John 20:28, as well as still express a subordination of Jesus to the Father throughout the gospel. The author may not quite fit into later theological boxes that were established, such as Modalism and Trinitarianism. Ultimately, we can only guess at the author’s views based on his text, so there is a chance that what he was thinking has been muddled by 2000 years of theology that has been constructed sense. Maybe the author felt Jesus was truly subordinate to the Father, but at the same time felt it appropriate to refer to Jesus by the title of “God” on a single occasion at the very end of the narrative. I think McGrath, for instance, brings up some interesting points about John’s Christology:
“For most first-century Jews, the distinguishing factor between the one true God and other ‘gods’ and heavenly beings was apparently worship. Jews had a similar cosmology to other peoples and religions in their day, but offered cultic worship only to the high God, to the one God who was the source of all other beings and above all others. Other figures who were not worshipped, whether angelic messengers or personified divine attributes, could share in the sovereignty of God and perform divine acts as extensions of the sovereignty and activity of the one God. This is significant for our study, as the focus in John (as we shall see below) is not the worship of Jesus, but Jesus’ participation in the activity usually reserved for the one God.” (James F. McGrath, John’s Apologetic Christology, 2001, p.76-77).
Thomas’ confession acts as a theological climax to both John’s narrative and christological project. It is not only the final confession. Although some (Keener, 1167) argue that Peter remarking “It is the Lord” in John 21:7 is the final confession. It is an explicit reference to the themes which the author(s) have attempted to convey throughout the Gospel, which Francis J. Maloney contend are thus: “the narrator’s teaching on the logos in 1:1-2, Jesus’s unique use of the absolute ego eimi…and his claim ‘I and the Father are one’ (10:30…)” (Maloney, 537).
It is often claimed that ἀπεκρίθη Θωμᾶς καὶ εἶπεν αὐτῷ ὁ κύριός μου καὶ ὁ Θεός μου at John 20:28 is an affirmation of Jesus’s divinity. But is this accurate? Does this mean that because Thomas said to him (εἶπεν αὐτῷ) ὁ κύριός μου καὶ ὁ Θεός μου that he was addressing a single person as κύριός and Θεός? Theodore of Mopsuestia didn’t believe Thomas was calling Jesus Θεός at John 20:28 (c. 350 AD).

Let’s explore this argument further. At John 14:9, Jesus says to Phillip: ὁ ἑωρακὼς ἐμὲ ἑώρακεν τὸν πατέρα and at v. 11 οὐ πιστεύεις ὅτι ἐγὼ ἐν τῷ Πατρὶ καὶ ὁ Πατὴρ ἐν ἐμοί ἐστιν. He’s saying that anyone who has seen him has seen the father and that he is in the father and the father in him, affirming their unity. This is one of the gJohn’s most important themes.

Interpreted within the context of gJohn, Thomas’s confession ὁ κύριός μου καὶ ὁ Θεός μου is addressed to the father in Jesus who has worked through him to raise him from the dead. Another possibility: ὁ κύριός is addressed to Jesus and ὁ Θεός is addressed to the father.

There are a number of reasons why this interpretation(s) should be preferred over the traditional one:

[A] When Jesus is addressed as “lord” in John the vocative κύριε is always used, not the vocative nominative ὁ κύριός.

[B] The arthrous ὁ Θεός μου cannot refer to Jesus because it would contradict the anarthrous Θεός at John 1:1b.

[C] Grammatically, ὁ κύριός μου καὶ ὁ Θεός μου is a TSKTS construction, which means that although it is addressed to Jesus, two different individuals are being distinguished. According to Sharp Redivivus by Dan B. Wallace:

“The papyri were seen, then, to be very much in step with the classical authors and the NT. Further, when a writer wanted to distinguish individuals—and there were scores of instances in which distinct individuals were in view—he or she invariably used a second article (TSKTS)—except, of course, when a proper name was involved.”

[D] The standard trinitarian argument that because ὁ κύριός μου καὶ ὁ Θεός μου is addressed to him (εἶπεν αὐτῷ), Jesus is ὁ κύριός μου καὶ ὁ Θεός μου, is a bogus one, since there are instances where, even when someone is being directly addressed, what is being said has nothing to do with the addressee. For example, ὁ δὲ ἔφη αὐτοῖς Ἐχθρὸς ἄνθρωπος τοῦτο ἐποίησεν. οἱ δὲ δοῦλοι αὐτῷ λέγουσιν Θέλεις οὖν ἀπελθόντες συλλέξωμεν αὐτά … (Matt. 13:28).

Conclusion:

Theodore of Mopsuestia was right. Thomas was really addressing the father when he exclaimed ὁ κύριός μου καὶ ὁ Θεός μου.