Well hold on now, broskis, I know things are looking pretty dark right now, and I'm probably blinded by hope, but the 3ds builds at PAX are apparently the final version of the game. These are playable behind closed doors, and only the press is allowed to play them, but maybe a channel like Game Xplain will check the "Press Start" screen for Konami's name. At this point, I'm 99.9% sure Snake isn't in, but who knows?
If Smash Bros does have DLC, which is definitely possible*, I'm pretty confident that Snake will make his Smash debut there.
*Mario Kart 8 is having DLC, and that will probably sell well since it has Link and the Villager in it,and the fact Smash 4 will probably be the best selling Wii U game, and one of the best selling 3DS games, makes me confident that Nintendo will seize the opportunity to sell DLC for Smash 4. If its character DLC, I think Snake has a pretty good shot at gettting in then if Kojima asks.