There's a pretty extensive API, capable of more than most games that advertise modding support, but it can't do literally everything anyone could think of, so people reverse engineer the game engine to make it possible to do even more things (hence it being called a script extender rather than the modding API). It's the mod reliant on reverse engineering the executable that break, not the ones using the modding API.
Imagine if Bethesda actually really listened to and catered to their modding community instead of just trying to monetize them. They would be legend right now.