Where I worked a sticker was placed over whichever EEPROMs were held configuration information. Some places would seal any IC, EEPROM, PLCC whatever electronic component it was if it was removable it was sealed. Even the doors to the logic area were sealed and locked, then the key for that door locked and the door that opened to get to that door was also locked away in a locked lock box that needed a key singed out from Security which locked it in their lock box.

There are many types and methods of security seal. I've used double-layered stickers that show VOID when peeled off. There are plastic tags that have a heavy wire that you wrap around then seal inside the cap. The wire would have to be cut using a pair of wire cutters. Any type of security seal would have a serial number known to company auditors.