Didn't stop them with Brawl, which even had freaking MGS4 music.A better question is, why would Nintendo want to promote Snake right now when his new game isn't even coming to a Nintendo platform?
At least this time around, Snake has a game on a current system (3DS).
Really, it's more a matter of Konami advancing their own interests, anyways. I have no doubt Sakurai is down for it, so if Konami is willing...
And from Konami's viewpoint, Snake in Smash is hype, and all hype is good for Ground Zeroes.