Ghost Chillies (or any other sufficiently "burn-off-your-mouth" chillies) are the answer. It's not high tech, but you're guaranteed to find the lunch thief (they're the one rolling on the floor), warn them off taking food from the fridge, and not have to put your employees through the "suspicion" deal.

I'm not sure what liability would be like, but technically, they're in the wrong for taking property that's not theirs. How were you to know that someone would eat your SUPER-MEGA-HOT pocket?