Well, if Kojima said "I can't talk about it for legal reasons," it wouldn't be much of a leap to assume:
A: He's got an NDA.
B: If he's got an NDA, Nintendo has contacted him.
C: If Nintendo contacted him, Snake is as good as confirmed.
So if Snake was in, and Kojima was under a NDA, Kojima would have to say something vague like "I dunno, I'm not working on it." If Kojima really doesn't know, he'd have to say something like "I dunno, I'm not working on it." Which is, ya know, exactly what he said. Factor in the massive troll that Kojima is, and... We have no clue.
*shrugs*