There's definitely punctuation missing. Phil's suggestion is the most likely one. Another possible option is to put the comma after "what," so that the sentence says, "What, does that make you an otaku?" This is a more colloquial structure, where "what" serves to make the question sound more rhetorical (showing that the speaker believes the answer to the question is obviously no). Some similar sentences with this structure: "What, are you just going to keep calling him?" (implies that the speaker thinks this is pointless or a bad idea) "What, you've never cheated on a test?" (implies that the speaker thinks this is either surprising or unlikely)

Hmmm… there is punctuation missing. We could use a comma or a period. It should be: "What does that make you? (Does that make you) an otaku?” In other words, “that” is the subject of the sentence, and “what” is the predicate nominative. “What” comes at the beginning, as is usual with question words in English. “That” refers back to the context, so I can’t tell help you with that. The question is formed with an auxiliary verb, in this case “does”, which goes before the subject “that” — this is known as inversion. Let me know if my answer helped you.

Which goes to prove the importance of punctuation...