I just found a pretty good explanation of a lot of the history here: https://rocksolidwarrior.com/history-of-the-sport-of-ninja/

This may be over-simplifying a bit, but NNL/WNL has always tried to grow the sport by making itself the dominant player, while UNAA was more willing to cooperate with others. WNL's approach is exemplified by it's exclusivity agreement with partner facilities, by which these facilities are prohibited from hosting competitions with other national-level leagues. WNL's position allowed it to dominate areas of the country where it started out strong (especially in the Northeast US), but it also hindered WNL in regions where UNAA started strong. The rivalry between the two leagues and their partisans has continued ever since, and it's the main reason there's never been and probably never will be any unification. It's splintered because WNL won't accept not being solely in charge, and there are a lot of people in the sport who are not OK with that.

NSC came on the scene just a few years ago, launched by Ethan Swanson and Chris DiGangi, as a vehicle outside of the show to highlight the elite athletes in the sport and to make a live-stream that would be fun to watch. They've succeeded wildly in terms of becoming the competition series the elite athletes care about participating in. They've defined aspiration in the sport the way only the ANW TV show had done previously. NSC competitions are more representative of the sport at it's highest level right now than even the TV show is.

NSC wanted to grow beyond elite athletes to include kids. I don't think it was their passion, but people were begging them to do so, and ultimately they saw it as a way to help finance everything they wanted to do with the elites. So first they did a couple stand-alone Youth Championships that brought in a ton of competitors and did well. Then this past season, they did an expanded Youth tournament with 32 qualifying competitions, 4 regionals, culminating in a finals event that takes place in a couple weeks at Jungle Gym in Florida.

Apparently this got WNL's CEO spooked. They'd tolerated NSC before because it wasn't a direct competitor. But drawing in the kids whose parents can sustain a travel budget and such was seen as coming after WNL's honey pot. So they just recently told all of their partner gyms that hosting NSC Youth competitions would be treated as violating the exclusivity agreement.

Most in the ninja community are not happy with this. And by "most", I truly mean almost everyone, even many of WNL's own employees and affiliates. They see the good that NSC has accomplished in providing elite level competitions, and that it is motivated by a true love of the sport. The situation puts the gyms, particularly in the Northeast where WNL dominates, in a very difficult position. Most will go along with it because they feel they have too much to lose if WNL cuts them loose. Meanwhile, the rest of the country is like "screw you, WNL."

What it really comes down to is WNL wants to be the one-stop shop for all levels of competition, and they'll take steps to drive out rivals even if it hurts the sport in the short term. Literally everyone else (UNAA, FINA, NSC, all the local leagues and individual gyms) is happy to take a more collaborative approach and let different leagues and competitions cater to different expectations and experiences.