Thomas derives from Aramaic תאומא (cognate with the Hebrew תאום). My understanding was that Aramaic, like Tiberian Hebrew, had the fricative [θ] as a conditioned allophone for the plosive [t], and that the latter would always appear at the start of a word. Why then was Thomas transliterated with a Θ rather than a Τ?
It is because, at least in the later borrowings, Semitic ṭ ט is regularly represented by τ [t], while t ת is represented by θ [th]. It has to do with the fact that the Semitic emphatics are unaspirated, while the plain stops are aspirated.
The fricative pronunciation of Greek θ, and of Aramaic/Hebrew post-vocalic t does not emerge until well into the Christian era.