Sounds like the airport had shut down for the night by the time he arrived. If it had been me, I would have just driven the rental home for the night rather than racing to the airport. A 3-hour rental is the same $$$ as a 12-hour rental (or as a 24-hour rental).

Presumably, they had an "after-hours" return box.

It might be worth sending an email to the manager. Maybe they would send you a coupon/voucher of some type, especially since they had advertised 1230AM as close time and they closed early.

As for waiting AFTER 1230AM for an "expected arrival", that might be a bit much. How long should they wait? 1AM? 2AM? What if the returnee had gotten delayed along the way and decided to just keep the car until the next morning.