I'd say it's worth it to use JoyCons even if you're emulating the games on PC. When they're not drifting, they're great controllers (if a bit cramped). I sold my Switch but I do miss the flexibility of holding my hands in whatever lazy position I wanted or using the gyro for aiming.

That said, it's trivial to use any other control or input device. You just might run into issues if a game requires motion control. I'm not sure but you might even get away with using a Wiimote, but I'm not sure what the controller support looks like there.

Since you're using your own Switch for this method (right? :)) then I'd imagine you could use your joycons?

How bad is it to just not have accelerometer? I personally tend to disable motion controls anyways...

It is sometimes part of the control scheme. For example, I was just playing a Mario game and you fling your hat by flicking the controller.