Yes, Magical Express runs until the last flight arrives. Bring the Magical Express Phone # with you. If your flight is really delayed late and noone is at the desk, you can call that phone # and you will receive transportation.
The last scheduled flight into MCO arrives at 12:26 am and the first scheduled flight out every morning is at 6:00 am. So by the time the folks from the last flight get delivered to their resort, it's just about time for them to start picking up folks from the resort for the first flight out in the morning.
I would venture a guess that there is at least one person going on ME from every single arrival and departure.