Except the silence of Yacht Club Games isn't entirely true (which potentially bodes even better for Shantae). They have mentioned that "Shovel Knight has a 0.001% chance of making it in Smash" either last year or this year shortly after Smash Ultimate was teased in March. I don't remember when it happened, but I remember the tweet. Probably still exists in their twitter feed.
If you follow the idea that companies are under NDA when making deals with Nintendo/Smash, we could infer two possibilities from this:
1. NDAs are less restrictive for companies whose characters are becoming ATs instead of playable fighters.
2. Shovel Knight AT could have been developed in-between now and whenever Yacht Club Games made that statement.
If you follow the idea that companies are under NDA when making deals with Nintendo/Smash, we also have to consider this:
1. Whenever companies/"important people in those companies" make explicit statements about their character and Smash Brothers (even if it is them expressing their support), their character is NOT getting in Smash (as this would violate NDA--you're not allowed, legally, to say either way without consequences). This would apply to Dante from DMC, Banjo Kazooie, and more recently, Sora from Kingdom Hearts (some people are interpreting it the other way, but they are clearly not aware of the implications that NDAs would have). There are probably others.
Also, on the topic of Indie Fighter games and the potential WayForward NCC (Non-compete clause):
1. Indie Pogo devs have officially confirmed that they approached WF to get Shantae in their game and were denied.
2. Blade Strangers devs have openly expressed interest in getting Shantae in their game as well, but she is not in.
Keep in mind that she is easily, by far, the most requested character to appear in these games--yet she has not. At least one of these occasions was because there was confirmed denial of having Shantae appear. It is entirely possible that the other two indie fighting crossover game had a similar occurrence that we are not aware of.
There is probably even more evidence, but this is what I could add off the top of my head.