I'm sure the emulators accept the Steam Deck's own accelerometer inputs for when you're in a non-detached mode, and tilting the screen to aim.
The super-mega-motion control games might not work, but part of what I mean by "works better" is that the Steam Deck can generally emulate with more power than the Switch itself, e.g., you can get a Breath of the Wild/Tears of the Kingdom setup with a better framerate than the switch itself, so, depends on what you want more. I don't have a lot of motion control games.
For ToTK in particular, this video suggests it'll barely hit ~30FPS on the Deck under Yuzu: https://www.youtube.com/watch?v=afetsBdQFyc
Whereas on a modded Switch you can run it at ~60FPS: https://www.youtube.com/watch?v=i6Z6W_AUNY0
There are other more recent videos backing this up and showing that the game has far more frequent stutters than on the Switch.
Anyway, the point is, I wouldn't dismiss sticking a picofly into your Switch as pointless. Even if you have no desire to inflict some Meta-style "fair use" on videogame publishers, it's still worth doing for perks like sys-clk, RetroArch, sm64nx and 2s2h.