Ah ok now I see the issue, not exactly sure why they allowed exploits to be used in official speed runs in the first place.
Because speedrunning is just about completing a game as fast as possible within a certain ruleset, they don't care if what they're doing is intended or not. For example in a half-life 2 any% run you're only allowed to use a keyboard, mouse, controller, etc for controls, no RAM editing or other cheating programs are allowed, and you're not allowed to use any console command which normally requires sv_cheats to be on, and you're not allowed to do any console command that loads another map. Introducing the additional rules like "No glitches" not only makes the run slower and not as exciting, but also makes it extremely difficult in certain circumstances to determine what is and isn't a "glitch." There are glitchless runs of many games, however those are much more controversial given the fact that as I said before, it can be quite difficult to determine what is and isn't a glitch.
There are even runs of half life, portal 2, etc that lighten up the restrictions even further, they allow for any console command that doesn't load a map. Those are much shorter and much less interesting to watch because they literally just noclip everywhere.
This is a valid speedrun under their defined ruleset. It's just not an interesting one.
Nintendo isn't going after them because they're using glitches. They're going after them because they're using emulators, completely ignoring the fact that there are legitimate ways to obtain a rom file from a legitimately purchased cartridge.
