Personally I started getting wrist pain 2 or 3 years ago. I have been using Colemak anyway for more than 15 years - my original reason for switching was because the German QWERTZ layout I grew up with is not very programming friendly, symbols like []<>{}/\ are hidden away behind hard to type chords. I found as a nice side benefit that my typing speed increased by 20-30 or so WPM... I did also have typing classes in school, so it is not simply because I started paying more attention to learning how to type with the new system.

After switching to a split keyboard my pain went away, and I think I learned that at least for me it was caused by exactly these symbols - on both US QWERTY and Colemak when you constantly type [];:{}| and so on, your pinky has to reach over to do it. At least for me that meant contorting my hand a bit to reach over. On my split keyboard all the symbols are behind a layer on the home row, and I barely use the pinky for anything, which fixes the issue. I also learned to hover while switching to the split keyboard, but that did nothing for my wrist pain when going back to my laptop's built in keyboard - after a full day of programming there the pain is back.