They are against emulators because they know the vast majority of emulator users are pirates.
But Nintendo also has absolutely no incentive to care if it's used for pirating. Users want to put in term of morality, when it probably doesn't matter much.
Even if there was no pirating angle, emulation is a revenue drain from old title they could bundle in the Nintendo Online subscription and remix as remake games (what we saw with the old Zelda games remade for the Switch for instance).
Even if people were using the emulator after buying the Switch and the actual games, that's still a stream they don't control (can't check if the game is played on multiple consoles for instance, etc) and there's nothing positive for them coming out of it.
On the other one can argue that people pirating does not improve their economics either so why risk it ?
I get your point – I just feel like there’s not a lot of potential economic improvement to be had here, but apparently there is.
But it's not as if corporations acted rationally anyway, they are led by humans and as such they are mostly driven by emotions.
And in case of game consoles, that also means they have to buy the hardware even if they only want to play one game. This is very significant potential income for Nintendo.
All my friends that are into games have a PS4/5 just to play exclusives, even if they play games on PC 99% of the time. And non-trivial number of them play XB3 in emulators so they don't need to buy a Switch just for that. If there is no emulators, they probably would.
All Nintendo did is make it easier for people on the fence to decide if they want to financially support them or pirate.