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It is their job, but, sometimes (I'm speaking in general terms, not specifically about Nintendo), it's better to pretend it doesn't exist, especially because of the Streisand Effect. But, if someone from outside tells them something exists, they might be legally obligated to take action in order to maintain certain legal protections on their properties in the future.

From what I understand this happened to Yuzu recently (and that's probably what this post is referring to), where, supposedly, some angry person found a bunch of Nintendo email addresses and emailed them all about Yuzu.

I've also seen it happen at least one other time, too. Cartoon Network used to have an old MMO called FusionFall (not FusionFall Heroes). It was shutdown several years ago, but a community of devs decided to remake the game, and they were even working on upgrading the graphics. They were making some really significant progress on it. Some guy apparently got banned from it, though. (It was in a public beta.) And they emailed Cartoon Network about it. Cartoon Network sent a Cease & Desist, and it disappeared immediately.