Supposedly, dwarves get unhappy thoughts from having no clothing on the UPPERBODY, LOWERBODY, and STANCE body parts. You might be able to go into body_default.txt and remove [UPPERBODY] from the humanoid plan's upper body, [LOWERBODY] from the humanoid plan's lower body, and then simply equip everybody with shoes only since removing all the STANCE parts actually causes problems. Strictly speaking, I don't think you actually need UPPERBODY or LOWERBODY tokens for a creature to work, so removing them might not be a problem. This change would make any humanoid critters somewhat harder to kill, as slicing off their lower body would no longer be instantly fatal, instead making that more like having a limb severed, but otherwise might work. It might make it impossible to equip torso or leg armor, though.
If that doesn't work, you might try moving the LOWERBODY token to the upper body so one piece of clothing would cover both the upper and lower bodies. This might make it impossible to equip leg armor.
If you try this and it works, please report back; I've been thinking about ways to reduce the number of required clothing pieces below 4, but haven't had a chance to test these methods.
By the way, if you remove every STANCE body part, I'm pretty sure a creature can't stand anymore, so that's why you can't just outright remove those to remove the shoe requirement.