I'm more skeptical than hopeful for a Banjo/N64 Classic tie in, despite really wanting it. I feel like the legal hurdles of negotiating for both Banjo in Smash and Rare titles on an N64 classic might be too much--at the same time, perhaps that would be the prime means of convincing Nintendo to allow Banjo on their platform, as I feel like Microsoft would be more willing for the Smash crossover than Nintendo, whereas Nintendo could be convinced that an N64 Classic with Rare titles will sell more (as someone with an N64, I know it's the only reason I would get one). I also think that it's rare for a Smash character announcement to tie in with an announcement/anniversary, though it has happened in small ways. Nothing comes immediately to mind, though.
I do feel, however, that if they do a N64 classic, now would actually be better than later. Their classic line on Switch will only start with NES titles, which means those who want NES titles can get them on the Switch, while those who want N64 titles would get the N64 classic--one wouldn't canabalize the other, in fact, both in tandem may make more business sense. Usually a classic console has been announced right after E3, so it is curious if it's happening that they would wait this long to announce it.
EDIT:
I agree completely. I love the thought of getting Banjo & Kazooie in the base game, Crash in DLC. We'd then have Nintendo characters, Sega's mascot, Sony's former mascot, and Microsoft IP all in one game. And that's in addition to Mega Man, Pac Man, Snake and Cloud, and it's crazy this is all a possibility.