To identify the subject of questions that use a form of be, the following two criteria can be helpful: subject-verb agreement and the case of personal pronouns used to replace noun phrases.
If ""What colour" is the subject of the sentence "What colour is your car?", then it should be possible to replace "car" with a plural object-case pronoun, such as "them", without changing the rest of the sentence. But in fact, we don't say "What colour is them?": we would instead say "What colour are they?", with a subject-case pronoun "they" and a plural verb "are", which shows that the singular noun phrase "What colour" is not the subject of a sentence like this.
The same arguments show that "What size" is not the subject of "What size is this shirt" (we would say "What size are they", not "What size is them?").
Because "it" in "What time is it" is a "dummy" pronoun, we can't actually replace it with anything else, but you can infer that is is the subject by analogy with the structure of other similar sentences.