I just leave my change where ever-- on the desk, in an ashtray, in a drawer. I've never had a problem with coins disappearing. I'll always leave something for housekeeping when I check out, most usually bills, but I too don't like carrying too many coins, and I'll leave them on the desk in plain sight as I leave.
I'm a little surprised that someone takes the coins. Either they misunderstood or it's a crafty employee dipping into the till.
Barry