I feel like Snake would be too much work for Sakurai and Namco. There's a reason why Mewtwo is taking so long to develop. Not only do they have to make the character, they have to worry about making the custom moves, fitting that character into modes like All-Star, and even having to record banter between Pit, Palutena, and Viridi.
They could easily reuse Snake's codecs from Brawl in Smash 4, but there's the problem of making new ones. David Hayter isn't a part of the series anymore and Takeshi Aono (Roy Cambell's Japanese voice actor) died back in 2012. They could rerecord lines for the codecs, but Kiefer Sutherland is expensive from what I've heard. I think bringing back Snake seems more of a hassle than it's really worth for Nintendo. I have doubts Sakurai will contact Konami again, but it'd be much easier to go with characters like Simon Belmont or Bomberman for Smash this time around. Might be smarter for Nintendo to just make DLC out of characters they own.