The only instance I can recall of a fan game ever being shut down was a fairly high profile (think OOT2D back in the day) Chrono Trigger project. Apparently Square contacted them and asked them to desist. Whether there was any basis in truth to that - numerous fan games have been sent similar, but bogus, e-mails from disgruntled fanboys - I do not know...
I fail to see why the big guns would get their pants in such bunches about humble fan projects - provided, yeah, they're not done for profit, obviously. How is it any different than fan art or fan fiction? No different, if you ask me. Just people paying tribute to their favourite game in their own way. Besides, there are a ton of fan games being made and are hardly being kept secret, and nobody's suing them...
All I know is fan games are looked upon by the wider fan communities in a different way than other fan works. Can't explain why. The crap thrown at the mere mention of a new fan project on some Zelda forums is bizarre. Ironically, they're ones who seem most interested in shutting Zelda fan games down... Especially when you consider how they lap up some of the !@#$%-poor fan art/fiction. And hentai. And Link/Ganondorf slash fiction. *shudder* Surely they're more harmful to a company's intellectual property?