I think Shantae could get in, Sakurai does whatever he wants after all, though from what I remember the producer or whoever he was (Matt Bozon?) seemed to advocate Shantae for "4 out of 5 Smash DLCs!" on Twitter.
I don't know if he would know, however, but since Way Forward was silent about Shantae's Spirit in Smash, I'm guessing he was as well. Given the new Steve, Master Chief, and Cuphead stuff, however, it probably means nothing, and she may still have a chance (especially since, being honest, I think Matt's tweet was deleted, so you could say he was backtracking like Aubrey and Rad seemed to do; this was before Joker was revealed, however, so maybe it was actually because he realized he made an error based on Piranha Plant, but idk). If we get a second fighters' pass, she and the others definitely have a chance, anyway.
In all honesty, isn't EarthBound considered niche as well? I'm not against Shantae, but from what I know EarthBound is more well-known with better sales and it's still not really well-known at all, generally, when compared to other franchises, outside of everyone who's played Smash Bros. and only knows EarthBound from it. I guess this could lean more in Shantae's favor...but it really just depends on how you look at it.