My partner uses these controllers that fit on the standard Switch and they find them much more comfortable for long-term gaming!

On a Switch Lite, you could get a bluetooth-connected controller that is more comfortable? Or I also found this grip that might be comfy!. There are tons of other cases that pop up, so it might be worth it to scroll through and see what would best fit for you.

I find my thumbs hurt after a long time of gaming pretty much no matter what. Practical tips like making sure the switch is propped on something, keeping your hand warm, and taking stretch breaks can help, but the pain sets in eventually in most cases. I hope you find something helpful for you!