my fortress features many of the Decapods being upset about not having shoes (which they cannot manufacture or start with, along with pants, socks, gloves, or many other things) allowing them only to have artificial shells, tunics, and coats.

0.3.3 - They can now make clothing for the relevant bad thought parts and will wear it by default. I have tested that they do this at least in a new save at embark, and that they will seek out new clothes to replace any missing spots. I have no reason to believe that it would stop working later, so it should be fixed.