@the100thmonkey An excellent example. The one I was thinking of is Prichard’s famous paper “Does Moral Philosophy Rest on a Mistake?”, the title of which has been copied over and over and over again (substituting other subjects for moral philosophy).
As for the MLA guidelines, the only rules I can find about question marks in titles are in regard to how to cite such titles. The possible existence of question marks in titles is simply passed over as an unexceptional fact, and there are no remarks forbidding or discouraging them. It seems, then, that they are no big deal one way or the other as far as MLA is concerned.