There are a few things to keep in mind when it comes to the various "theories". Not all are created equal, and some are crafted to support particular picks for Smash, as is much of Smash speculation.
Music theory was based on the idea that the music reveal schedule would signal particular series getting particular characters. This idea also suggested a larger set of newcomers compared to what we actually ended up getting. I would argue that's why a good number of people believed it.
Box Theory was effectively the opposite. This particular theory was not just based on leaks, but actual logic. Based on the layout of the box itself, it was believable that the two remaining highly speculated newcomers of the time, Ken and Incineroar, were the remaining two, especially when things lined up perfectly with Ken sliding in next to Ryu in order. That's probably one of the only concrete "theories" to exist imho.
Partner theory is pretty much a reach, considering the logic somewhat jokingly posted before being, "Oof, that character doesn't have a partner. We can't add them!" It's also interesting that the definition of "partner" changes depending on the character. Sure, Hero and Joker have Slime and Morgana respectively, but Kazooie isn't the same thing as Morgana and Slime. She's an active part of the moveset, far more than Morgana is, or Slime is poised to be.
I don't even know what other theories there are but the last one I'll talk about is more based on actual information, but could still be disconfirmed.
Mii Costume Theory is based on the concept that Mii Costumes will only be shown off in combination with a character getting revealed from the particular company missing Mii costumes are coming from. So for example, considering Hero comes from Square Enix, and there are still Mii costumes to be revealed that come from Square Enix like the Chocobo Hat and the Geno costume, then it's speculated that when fans get insight on the 4.0 update and further Hero information, the Square Enix Mii Fighter costumes would get revealed.
For the record, this is exactly what happened with Mii Fighter costumes that came from SEGA when Joker was revealed. Atlus is owned by SEGA, so that can be easily explained.
The Mii Fighter costume theory can easily be disconfirmed or disproven if costumes for any franchises/companies are revealed without a character reveal. So this could be something like Hero and 4.0 update, but in addition to Geno and the Chocobo hat, Mega Man X, Monster Hunter, and other Capcom franchises would be revealed as well.
However, it does stand to reason that if Hero is covered, as is 4.0, and only announces the release of Square Enix Mii Fighter costumes, the theory itself is bolstered a tad. If Banjo comes with the 5.0 update, which is accompanied by Banjo-Kazooie costumes, along with other Microsoft owned IP represented in this fashion, then I would say it looks pretty strongly supported.
As I said before, this can be easily squashed. But for the time being I think it's worth being considered. It just shouldn't necessarily dominate speculation.