This is easy for Apple to do since every iPhone is serialized with the serial number on the outside of the box. It's trivial for Apple to log the serial number

This is easy for Apple to do since every iPhone is serialized with the serial number on the outside of the box. It's trivial for Apple to log the serial number of every phone sent to a store. It's also trivial for Apple to record every serial number that was legitimately purchased or used to fulfill a Apple Care claim. It takes an employee a little bit of effort to scan the remaining stock, but once they have the list of what they are supposed to have in stock compared to what they actually have in stock they know exactly what serial numbers are missing. It's also useful to de-incentivize regular theft from an Apple Store. It's a pain to do this often enough to catch low quantity type thefts, but if a manager opens their store and realizes that someone stole 100 iPhones the night before, then it's definitely worth the effort to figure out which serial numbers were stolen and track them. It's also worth it to investigate the employee that didn't lock up properly the night before. Stolen phones become much less valuable if word gets out that Apple tracks them. A stolen phone still has value as parts, but the value has gone down quite a bit.