I just had a thought that there's really no reason for Snake to be cut except for one (crucial) reason that could go either way.. Let's look at all possible influences.
I doubt Sakurai cares about purity or whatever (he wouldn't have gotten Sonic and Mega Man lol). If Snake is cut, do you really think he just sat down and thought "we don't need Snake so let's cut him."? Considering his distaste of cutting character and friendship with Kojima, obviously not.
Kojima ad Konami have no reason to refuse. This is free publicity, and Kojima has wanted Snake in Smash since Melee. Kojima's comment actually makes me think Snake got in because it sounded too playful and playing with our minds...you know, what he always do.
It all hinges on Nintendo's permission. It's 50/50 because if they gave him the OK before, so it's not like they necessarily care a character that isn't so associated with Nintendo (like Sonic lol) is gonna get in Smash. (It's a benefit actually, some will buy the game for Snake.) On the other hand Nintendo was winning the market so they didn't have anything to loss were as they're in a big decline now, but the thing is Snake isn't exclusive to Sony anymore so there really isn't much lose. MGSV's character is Big Boss, not Solid Snake.
A big thing going for Snake's inclusion right now is that he hasn't been deconfirmed yet. You'd think if a big third party character who has been a Smash game before got cut we'd already know that by now. There's no reason to keep people in the dark about it if he isn't in, Sakurai could easily just downright say he won't because there's no loss in that and no benefit from keeping his exclusion a secret.
I'm confident in his return, but at the same time, Nintendo could say no.