Nintendo just seems to prefer developing stuff without bothering to conform to a spec. They're happy to start with an existing standard as a base, but they'll build on top of it however the heck they want.

I agree, it doesn't seem to be malicious. Consider: it would make sense if Nintendo tried to prevent third-party controllers, but—while the Joycons certainly don't use DirectInput—the protocol doesn't seem designed to lock anyone out, and there are lots of third-party Switch controllers.

anti-cheat is a big motivator.