I doubt that Nintendo was aware of any of that, aside from maybe the Patreon, when they decided to initiate the litigation process. The Patreon was admittedly risky, but as far as I can tell the settlement states that the emulator itself is illegal as per the DMCA, regardless of whether or not they were making money off of it. If a precedent is set here, it is quite dangerous.

> Also, doesn't Yuzu itself include pre-decrypted ROM dumps from the actual Switch hardware, like for example the OS bootloader ?

As other commenters have pointed out, Yuzu did not include any Nintendo copyrighted assets, so this is wrong.