I suspect Nintendo cares mostly about primary entry points, and that's why we haven't had a stability update lately.
Anything else is going to pose more inconvenience than 95% of users are going to want to deal with, honestly. And that last 5%, those who keep up with the scene, requires a lot of effort to stop. It's just not worth it.
We're not in DS territory where everyone is doing it. Even with OoTHax and this new one, it's still a pain in the ass with an updated system. As long as the primary entry points like BrowserHax and TubeHax and IronHax are dead, that may be enough for Nintendo.