The keys are nintendo proprietary code though, which I'm pretty damn sure is copyrighted
It's not, because the keys are too trivial for copyright.
and before you counter with you can't copyright a a string of letters and numbers you can copyright the order they are in.
A random number that takes a fraction of a second to generate is not copyrightable. There have been DMCA anti circumvention cases thrown out because they were just allowing interoperability, but if the keys themselves were copyrightable then they would have succeeded on that. But they didn't. So it's pretty clear that keys can't be copyrightable, google "illegal numbers" and you'll find some examples.
Which again, isn't in Atmosphere, so they cna't do anything about it. The only thing Atmosphere does is violate the terms of use
It's involved in DMCA violations. If Nintendo wanted to get nasty they could involve Atmosphere in a conspiracy charge with TX and possibly also gbatemp for hosting/linking to the patches and installers which allow NSP to be installed.