Certain times of year in MCO can be very heavy and they may run short of cars late in the day.

If you are going to be late, it would be best to call the office and tell them your "flight is leaving late" so they will try to hold your car.

You should also keep looking at rental rates, as they may get lower between now and your trip. I've often saved hundreds of dollars doing this, and then you just assign the proper time for pickup since you know you flight times.