Isaac will never be in a Nintendo game, especially not one rated E for everyone.. it's entire game is literally a series of blasphemous references you act out. if it was some very very subtle thing in one or two levels it could be edited for release, but the games entirely is literally just that. so no, Nintendo wouldn't go anywhere near putting that in smash bros.
as for shovel Knight, even tho this game is a salute to Nintendo, and absolutely E for everyone, I don't think it would make it into smash either, just because it's a new indie game. smash bros characters are either Nintendo characters the developers feel close to, or characters from other franchises who have long proven themselves. This is Ryu, Cloud, Pac Man, unarguably characters that have proven themselves over a decade later. and so for this reason I don't believe shovel Knight, as cool as he would beb, will show up in smash, at least not anytime soon.