They do by counting the money at different points in the day like shift changes and close...

I had this happen once when I worked at a shitty movie theater I misplaced 20 bucks and for the next two weeks they followed me around doing random tasks... At the time I thought they were really stupid and I mean it was... But now a long time later I know they wanted me to quit but wouldn't fire me...

I showed them I didn't have the money but whatever they do check is all in saying