Nintendo regularly sends DMCAs to rom sites hosting roms for old systems. Vimm's Lair has gotten hit a bunch of times. Some sites fly under the radar or are in jurisdictions where it is harder to issue takedown notices. IIRC The Internet Archive specifically has a special DMCA exemption that gives them some leeway, but they can still be sued and have been forced to take down things like issues of Nintendo Power and roms in the past.
I feel like you're just being pedantic if you're going to try and argue Nintendo requesting Valve not allow Dolphin in the Steam Store citing the DMCA is not "blocking" Dolphin from the Steam Store.
Maybe I didn't explain it very well, so let's start with the basics:
Naively, we could say Nintendo loses money from retro piracy, and therefore they should shut down all rom sites, just like they did with LoveRetro. But this brings up the question, is Nintendo just too lazy to search "roms" on Reddit? Why did they never take down Myrient? The obvious reason presents itself: lawsuits cost money, and more importantly takedowns cost goodwill. The reason why that matters is goodwill drives sales (in fact, goodwill is Nintendo's greatest asset, just like it is for Apple, as strange as that might sound), and therefore goodwill counts as money in GAAP. Every time Nintendo considers taking down a rom site, emulator, or fan project, they need to ask themselves a question: will this help us or hurt us? As a layman, how much money do you think Nintendo loses from retro piracy, and how much goodwill do you think the average takedown costs them? Also, consider the fact that Nintendo's first party Wii titles are probably more valuable than Sony's entire first party retro library. Consider the fact that Nintendo is more able to weather these sorts of "bad PR" moves because of their more devoted fanbase.
Of course, these are not the only considerations, games companies also benefit from retro piracy, emulation, and fan projects, because these keep the brand relevant without them having to do anything. They also provide other benefits, for example Nintendo was proven to have downloaded a pirated rom of Super Mario Bros for sale on Wii VC, and Nintendo undoubtably used AM2R as a way to gauge interest in and gain free marketing for their own Metroid 2 remake. It should be pretty obvious from the things I've mentioned that the analysis skews towards taking down current gen roms and such, and away from taking down retro roms.
But of course, even this is too simple, after all, Nintendo does take down retro roms sometimes, what's the missing piece? If Nintendo is seen to approve of a rom site existing, this can be interpreted by the court as giving a general license to the public to pirate their games. That doesn't mean it will be, but Nintendo cannot afford to take that risk. Therefore, if Nintendo can pretend to be unaware of a retro piracy site, they will ignore it, and if they can't, then they are forced to take it down. A former Nintendo lawyer actually explained this principle 2 years ago.
https://aftermath.site/pokemon-lawyer-cease-desist-fan-project-pikachu-movie/
LP: Before we wrap up, as a games journalist who has covered the scene extensively, this is something I've always wondered and have never got the chance to ask: how does The Pokémon Company handle Cease & Desist letters with regards to fan projects? How did you find them, and where did you draw the line on what's allowed and what the company thinks needs to be shut down?
DM: Short answer: thanks to you folks. I would be sitting in my office minding my own business when someone from the company would send me a link to a news article, or I would stumble across it myself. I teach Entertainment Law at the University of Washington and say this to my students: the worst thing on earth is when your "fan" project gets press, because now I know about you.
I probably don't need to explain why the distinction I pointed out with regard to Dolphin matters, but if Nintendo gave permission to Dolphin to exist in the way that they currently do, that could potentially be interpreted as giving up the right to sue over any decryption of Nintendo games, even current gen, which is something that they cannot risk, which should be very obvious from the Yuzu lawsuit. In actual fact, if Valve had never asked permission, Nintendo probably would have completely ignored Dolphin being available on Steam, just like they ignore it being available on Google Play (and would ignore it being on the App Store if Apple allowed JIT). Valve asking for permission put them between a rock and a hard place, because they could not give permission, and they also really don't want to take down Dolphin, which should be very obvious from the way they handled the situation. They were forced to choose an option which admits they are aware of Dolphin (and therefore they probably will be unable to sue them in the future), while still asserting their rights with regard to digital locks.