At the end of the day, Kojima is irrelevant to Snake getting into a future game. So it really really does matter when it comes to Konami. Sakurai can't request anything to Kojimi during Smash 4. Kojima doesn't own Snake at all. He has no say. Of course he wasn't approached. That's just basically how licensing goes. There's no blessing to really worry about, as at most, if Snake were to get in, he might let Kojima know as more of a friendly thing. But it's still business.
Whatever reason Snake didn't get in 4, which we really don't have a clue about either, it's not simply "Sakurai didn't ask Kojima", or for that matter, that wouldn't have happened either way. The guy has no say anymore. He could request Snake come back at best, and Sakurai can only confer with Nintendo and Konami about it. Whatever happens after that is what it is.
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On another note as someone who pays a lot of attention to story writing; Bosses are not inherently Villains. They're only Antagonists. Antagonists can be a Villain or a Hero. Same thing works with a Protagonist. A Heroic Antagonist can exist(in fact, Sonic Adventure 2 is a great example of having quite a few of these. In the Dark Story, Sonic, Knuckles, and Tails are Heroic Antagonists to fight. In the Hero Story, Rouge is an actual Heroic Antagonist, as she strictly works with the good guys and is pretending to be a bad guy. She's a dubious hero, by all means, but still actually one. Shadow, Eggman, Gerald, and Biolizard are the actual villains of the game. G.U.N. is also designed to be a Heroic Antagonist(despite seeming neutral, anyway. The only time they're actually Villains is Sonic X outright, and only some members), and Amy just kind of... is there, among the various story characters. Things do change slightly when Shadow's game releases, as Gerald is now a Heroic Antagonist too, but that's due what was basically a minor retcon in the backstory. All they did was give the Eclipse Cannon another reason for existing and Shadow's backstory was expanded. ...It's also the only game where Shadow can be a Hero or Villain willingly depending the route(so it's never set in stone. There's not even an official route that ties to the final story, just theories).