Heck I had to keep track of every firearm, mortar, machine gun, bayonet, kabar, piece of night vision equipment and every piece of ammunition for a Company of Marines (a few of them with sticky fingers) that only wanted to get released from the Company area so they could go get drunk. And I never lost a thing. But, I was motivated to pay attention because I wanted to go to the NCO club too.
It seems to me less a matter of how to take care of this stuff and more a matter of everyone involved being properly motivated.