Problem is that a lot of people have decided to make let's plays and streaming there career so even though Nintendo does have a right to collect Revenue the let players do everything they can to make them look bad or not show Nintendo content which has hurt Nintendo from a marketing stand point due to the increase in people watching Live Streams and Youtube more than more traditional media were Nintendo can more easily control advertising.
Well the main argument for YouTubers is that let's play falls under fair use which states that Nintendo doesn't have a right to collect revenue on somebody else's commentary video, even though Nintendo games are being used.
The thing is that legally it's a rather grey area that nobody really knows. Developers are still able to take down videos however because of YouTube's fairly terrible anti-copyright system that shoots first and asks if you were actually guilty later.
It's all ultimately dependent on if Let's Plays get to enjoy the same fair use laws that things like game reviews do. As far as I know, there hasn't been any major legal rulings on the matter and it's been entirely up to YouTube to decide who is in the right.
In either case I think right now at least it hurts you to go after YouTubers because you lose that free advertising and it's seen as a greedy move in the eyes of a lot of people. Given that indie devs are more than happy to have somebody throw up a video of their game and get all those free views, I don't think we're ever going to see it going away. The major devs might win for their games, but all that will mean is that people avoid playing their games in videos.