Really poor analogy. Nobody makes money off of ROM's of 15+ year old out of circulation games, and the publishers lose no money either because those games are no longer available new. Comparing the Emulation of 15+ year old consoles to modern day game piracy just doesn't work. Nintendo just struck a huge blow against game preservation efforts, because they just set a precedent that is causing other ROM sites to close.
This has nothing to do with game preservation. Nintendo is protecting the rights to their own IPs. And yes, people still do make money off 15+ year old games. See NES Classic, SNES Classic, Flashback Consoles, previous iterations of Virtual Console, etc. Nintendo, and @Games did go through the trouble of making sure they went through the proper licensing channels to put games on those systems for a reason. If the ROM sites were these altruistic, philanthropic entities selflessly concerned only with preserving niches games that aren't available in the wild that you make them out to be; there wouldn't have been any Nintendo IP's on those sites in the first place. And then, Nintendo wouldn't have a case against them.