The legal dubiousness of bundling keys was already well established, emulators for Nintendos other recent systems (3DS/Switch) don't include the keys, and instruct the user to dump them from their own hardware to shield the project from liability (of course the keys can easily be found online, but the projects don't endorse that out of abundance of caution).
I think people should just share roms with the encryption pre-removed and that's would be the end of the legal reach for Nintendo here.
Not sure why we still reproduce undesirable code from the console.
In another timeline where the Wii was jailbroken earlier the standard might have been to distribute decrypted versions, but that's not how it worked out.
https://en.wikipedia.org/wiki/An_Open_Letter_to_Hobbyists
whoops wrong link but fuck it, serendipity
Maybe retroarch itself doesn't emulate anything, but just provide a render surface/input abstraction to 'cores'?