And thing is it's really only been fan games that have been shut down, I've yet to see any fan films or tech demos taken down. "Majora's Mask HD" fan trailer's been around since 2012 and nothing happened to that, neither the Zelda x Ghibli fan trailer, and hell "A Fox in Space" has been left alone ever since the creator made it 100% clear it's completely non-profit and self funded.
Fan games I can understand because you could make the argument they act as a "free replacement" for Nintendo's ultimate bottom line, which is providing games you can't get on platforms other than their own. Fan films are a different story as they can't replace the experience of an interactive game, I think the only thing Nintendo cares is "is it making any money off our trademark?" and if it's not they leave it alone.