Download pkhex and add as non-steam game
Open settings and check "force use of compatibility tool. It doesn't matter which version of proton you use.
Run pkhex through steam. An error will pop up linking you to the .net 7 download.
Locate the compatibility data in steam/steamapps/compatdata. It'll likely be the most recent one. Keep this window open.
Download and add the .net 7 installer and run.
After .net 7 finishes installing, copy the files from its compatibility folder to pkhex's compatibility folder. Pkhex should now run on steam deck.
Bugs: when clicking on a field that can be typed in, the steam keyboard will flicker open and closed. This is less of an issue in gaming mode. It is difficult to scroll through lists without an external mouse and keyboard.