I was the main developer and webmaster of Zelda Classic for several years in the mid-2000s. Nintendo knew about us because disgruntled users reported us in retaliation for forum drama, but they never came after us. Probably because we were never prominent enough for them you care, but we liked to imagine we were protected by someone high up at Nintendo.
I wonder if you'd just been around since before Nintendo got so extreme and were grandfathered in. If Nintendo will take down the likes of AM2R and the Unreal Engine remake of Bob-omb Battlefield they'd certainly take down a straight copy of Legend of Zelda.