Yeah, as long as they have your flight info, they'll know when to expect you. Just put down a good guess as to when you think you'll show up. Just did a quick check of Avis, Hertz, and National, and all are open 24/7. I'm sure most/all of the other brands are as well.

Last time I rented at SFO (last summer) I arrived about midnight and there were probably 30-40 customers in the rental car center picking up cars.