My guess, based on dealing with DMCA notices in other contexts, is that Nintendo doesn't decide at all. They hire a third party who scours the internet for stuf

My guess, based on dealing with DMCA notices in other contexts, is that Nintendo doesn't decide at all. They hire a third party who scours the internet for stuff that might be infringing and that third party uses automated tools to fire off complaints and notices without anyone at Nintendo even being aware of any one particular instance at all until after it starts generating bad press. Youtube gets the notices and, without anyone at youtube ever being aware of any particular instance either, Google's automated system is what actually takes down a video. It's all automated systems sending notices and automated systems carrying out take downs, with companies who are routinely careless about sending DMCA notices on one end, and on the other end you have one of the richest corporations on the planet who still can't be bothered to pay a human to double check before they ruin someone's livelihood, or even to help clean up after their automation screws up.