The way I see this, it's Nintendo rejecting the "research" that the youtubers are doing, because, lets face it - most Nintendo IP's don't have a decent story, it's way more about the experience of mechanic, like Super Mario or the social experience with friends, like Mario Cart. Therefore there should be some value in watching the way youtubers are playing and watching the feedback that they get in the comments. Even if the environment isn't completely controlled, I reckon they should still be able to gather insight from it.
And for the for this news with hacked roms etc, they should be looking at it going - "hey, someone is doing something with our game that we weren't considering, maybe lets look into that and see where this moves." I don't see Nintendo making less money by people using hacked roms etc. It's so so banal that they feel they must defend everything, all the time, despite it making sense or not.
Furthermore, there is a problem when you're trying to battle your customers and overly aggressively enforce copyright while holding the "this is infringing on our potential product margins." It adds a degree of desperation to the mix as well. To me that just puts them in bad light. I used to actually like Nintendo, and I would tell my friends that if they wanted good gameplay they should consider a Nintendo product over MS or Sony products for their kids. Now that has very much been reversed, because I can't with good conscience recommend someone to buy Nintendo products anymore from a political point of view, I simply believe that living in the modern world you need to be modern, and Nintendo with their archaic business practices are seemingly refusing to.