I've always assumed when they scan your boarding pass at security, the system registers you as having gone "airside". Then, when they scan it at the gate, the system registers you as having left the terminal and boarded the aircraft. This means they know at any one time who has checked in for a flight, and of those people, how many are airside and therefore ready to proceed direct to the gate. I assume this is what prompts the announcements about passengers travelling on such and such a flight who have not yet gone through security to do so. They can match up departure times with waiting times at security etc. When they're about to close the doors, and someone hasn't turned up, they know from the scanned boarding passes whether they're airside or not. It also means if you check-in online at home, they know whether you've actually made it to the airport.