If you don't, then the area under the hinges will not get blasted or most of the area where the door bolts on.. I f you do remove them you will have a cr full of san so it's a personal choice.
When I disassembled my car the area behind where the door hinges bolt to the body were covered with surface rust.
I would recommend taking every last bolt off the car, my thoughts are, if you're going through all the trouble to have the car media blasted you should have as much stripped to bare matal as possible. Just my 2 cents.
I agree with m-dave you will have a much harder time getting the media out of all the nooks and crannies.
Shoot, leave 'em on, take them off when it gets back and hit it with a knotted wire cup brush on a 4" grinder. Once they're off, it'll take about 5 minutes to take those spots down to bare metal. Plus you don't have to worry about them dropping the doors or deck lid. I'd at least leave the doors on.