Jennifer Crumbley was found guilty of manslaughter for doing nothing to prevent her son from shooting up his school.
That was criminal court with a much higher standard than a civil case.
Nintendo has consistently been one of the strongest protectors of their IP, and a defense that says “We tell users not to commit piracy” is about as effective as a sex workers disclaimer that “money is exchanged for time.”
Software developers should not be held liable for what their users do with the software unless the software itself does something illegal (such as malware that gains unauthorized access to secure systems). If developers were responsible for their users then you would have all kinds of bizarre lawsuits. You would be able to sue Microsoft for things written by users in Word. It wouldn't be a stretch to sue Linux contributers because someone used the OS to perform a DOS attack or to host a scam site.
I think Nintendo would be banking that the Yuzu team likely had lax (if at anything) policies and processes for compliance to their public stance on piracy.