Sakurai and Kojima being friends can really be taken either way.
On one hand, Sakurai would be more likely to include Snake again due to their friendship, but, at the same time, Kojima would likely be more apt to understand that Snake only got in due to a very generous favor and wouldn't hold it against Sakurai if he weren't included again. Though, regardless, we're nowhere near the juncture where we can just blatantly say that Snake is or isn't in the game. If I had to guess, I'd say that the odds were in his favor rather than against him, but not leaning heavily either way.
Even if he's not included, he'd be great DLC material later on. I just wish Kojima would start repaying the favor and putting more MGS games on Nintendo systems. "Thank you for putting Snake in Brawl! ...oh, what's that? MGSV should be on the WiiU? No, that's silly. Thank you for the free advertising, anyway." If I didn't know any better, I'd say that Sakurai got punk'd.