That depends on the context. If the question was "Are you not perfect?" or if some said about you "You are not ideal" ("Du bist nicht ideal"), then the correct response would be a positive statement: "Doch, ich bin perfekt".
No it doesn't. Questions take that form but are marked with a question mark. You can flip the noun and verb any time and it still makes sense. For example, Ich weiß nicht = weiß ich nicht. Also: Nein weiß ich nicht.