I don't have any personal experience running Switch games on the Steam Deck, but I do have experience trying to use the Switch Pro controllers. I think they may work fine for some people now, but I have never been able to have them have a stable wireless connection. But when the connection was established, the accelerometers worked fine. (I gave up and just bought some XBox controllers.)

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.