Well let's see...
1. Shantae did decent on the ballot, at least in the west. Characters who did about as well or even much worse in some cases still received notice in the form of DLC mii costumes, amiibos, or appearances in Ultimate in the form of an assist trophy. (Shovel Knight, bomberman, geno, ashley) Since from what we know, Shovel Knight was also only really popular in the west, it means you don't need to be popular in Japan to get recognized. The speculation here is that if others with the same popularity got recognized, Shantae should too.
2. Wayforward was very vocal during the 2015 smash ballot but went radio silent about smash after the ballot ended. We now know that the roster was finalized at the end of the ballot so their silence would make sense if an NDA was signed. There is no way to confirm this, however. I'd also like to add that they often respond to questions on Twitter but will not if it's smash related. They responded to a tweet asking about their lack of presence in Indie fighters but stopped responding as soon as smash was brought up. Some also think the fact that Shantae isn't showing up in any of the indie fighters is because she may have signed into a contract preventing her from being in other fighting games as a playable character(assuming she is playable in smash)
3. Matt Bozon recently followed Sakurai on Twitter in the last month. It doesn't mean much on its own but worth noting.
4. The pajama DLC involves you going from level to level gathering people for Shantae's ULTIMATE slumber party that everyone's invited to. During the ending she says she's going to move it to RISKY'S SHIP and Mimic tells her to get rest for tomorrow. When asked why he leaves it on a cliffhanger with, "Who knows, tomorrow is another adventure." This could mean absolutely nothing but in the context of smash is quite curious, especially considering much of the suspicious writing is in bold. I take it as, assuming it's smash related, that she's joining smash and Risky's ship is her stage. Also, the timing of the DLC is weird being a free major content update released almost two years after the game's initial release. If it had released a month earlier before the steam summer sales it would have made more sense.
Everything else is mostly just statements about Shantae's history with Nintendo and popular indie status making her a potential pick for a 3rd party character. So yeah, it's easy to see why she might get into smash but at the end of the day it's still entirely speculation and fan theory. It's not like Geno/Skull Kid who got mii costumes or Shovel Knight/Bomber Man who got amiibos after the ballot. Shantae hasn't received any kind of public acknowledgement from Nintendo which kind of worries me.