Technically, he announced the C&D, mentioned he may try and change things up to keep the game going.
Nintendo has sued people for less. And its usually followed by gag orders, so people can't say anything about it.
Disney does it as well. The Patreon technically meant he was paid for the game, so it wasn't freeware.
Nintendo could have had someone watching his Patreon, and pushed things forward after he called them out. That is bad rep waiting to happen.
Patreon also gets orders and things if someone breaks copyrights.
His page is still up. But, who knows what happened there.
The fact that copyrights can do this to fellow like him, is annoying. I doubt it was tarnishing their reputation.