What part of NDA don't you guys seem to really understand? I'm sure the guy's aware of where his intellectual property is being utilized pretty much at all times, so him giving a neutral answer just says 'I know but I can't say.'. That's the point of an NDA. You're not supposed to give ANY information, not even answer yes or no questions, 'cause that can give away information meant to be kept secret.
So Kojima says 'I plead the fifth.', well, you guys take it however you want to take it. No-one's going to be surprised if Snake is back, and no-one's going to be surprised if Snake is not. As far as I'm concerned, Snake was a fluke, a guy fulfilling the wish of his buddy and doing him a solid. There was pretty much no valid reason to have Snake in Brawl and, honestly, there's no valid reason to have him return, either. But I digress.
tl;dr: Kojima's neutral answer was because NDA; don't hold your breath for Snake's return, but don't be surprised if he does, either.