No, their utility is balanced by the research investment/cost in mage time/gem cost or whatever, especially if you want to wish (or other high level spell-spam.)
Maybe the simplest solution would be to give the gem producing items a small (like 2%) chance to wear out, so that you cant have too much of them. If there would be a 2% chance, a clam would exist approximate 50 turns, so you pay 20 gems and get 50 back.