timetokill
Banned
It legitimately wouldn't surprise me. They let it go for years, just like they do with most fan projects. This game was never hidden or under the radar, and it has had multiple substantial demos available. They didn't do anything about it until fully released with reception positive enough that it resulted in some major publicity (for a fangame, at least).
And I think you would have to be crazy to think they didn't know about it until now. There are tons of videos of the demos on youtube dating back a few years, and Nintendo manages to find much smaller projects that "break rules" like plugging donations. There's no way they just found out about it.
I hadn't heard about it until it released. I'm on here a lot. I wouldn't say it's impossible for them to not have known. Furthermore, there are like a million fan projects like these that never release. I doubt they have the ability or desire to shut down every one of them when the majority don't actually come out.
In the end, yes, it sucks for fans but it's also incredibly predictable and avoidable.
If you want to know whether something is taking advantage of an IP, consider this. If this guy had made this exact same game but without Samus, Metroids, or the name Metroid itself, would it have gotten this kind of recognition? The answer is: of course not. People care because this is a "Metroid" game.