Will damaging an enemy with explosives damage or destroy the loot?
Explosive weapons (such as Launchers and thrown Grenades) will only destroy the equipment of a target when they are the killing blow. If they only injure a target with an explosive weapon this causes no damage to their equipment and they will still produce a corpse if later killed. They are even still available for live capture.
A quick explosive to destroy cover followed by a hail of gunfire is an effective take down measure, and won't cost you any of the materials you could expect to obtain.