Costco evening employee here:
Yeah, we check those at closing time. As well as behind the mattresses, the bathrooms and anywhere else someone might reasonably hide. There are generally people stocking stuff for 3-4 hours after the store closes and from 5 hours before the store opens in the morning.
There's a small window when the place is completely empty, but it's only from about midnight to 4am.
Well, better than the time someone broke into the home of the Canadian Prime Minister (Jean Chretien at the time) and his wife held off the intruder with a soapstone carving...