A bit of optimism.
I got this idea from that one youtube video that was heavily supporting Shadow for Ultimate. It's possible that Sakurai might have seen all the votes for indie characters on the ballot and decided that he wanted to add an indie character. If this is the case, Shovel Knight would end up being the gift that keeps on giving. It could mean that, should he want to include an indie in the game from the outpouring of support, that Shantae may have actually absorbed all of Shovel Knight's votes from the ballot. And there actually is a precedent for this too.
Sakurai noted that, of all the requests for Final Fantasy characters, Cloud received about 1/4 to 1/3 of all the votes. Given the phrasing, it appears as though he was intent on representing Final Fantasy in some capacity due to its presence in the ballot. The only drawback here is that indies are multiple different games whereas Final Fantasy is one series (with a lot of clout). However, if you were to roll all the indies into a single category, it starts to gain some clout of its own as an entity. So to that I would say it entirely depends on how Sakurai sees this.
If he sees all of the support as a collective push for an indie character, Shantae might absorb all the other indie votes. If he sees them all as separate games and franchises, she'll get none of them. I think in the former's case it's helpful that there is a bit more homogeneity than is typical amongst franchises (given all of the cross-overs, indies direct and indie section). I don't know, it just seems like something to chew on.
I think we can reasonably expect that, between Shovel Knight and Shantae, they took a very noticeable chunk out of the ballot (not to mention whichever other indies were voted for). And I could see why Shovel Knight may have been shelved for this iteration (considering he only existed for a single year at the time of the ballot). Shantae, having been around a lot longer and being the, likely, next most popular indie character (or possibly even the most popular given her worldwide presence; who really knows?) would have been the most logical character to absorb all the other votes.
And then she ticks every single one of Sakurai's boxes for a newcomer in spades...
I'm just saying.