I don't think it makes much difference. If you have a smaller cutter you can move the cutter faster; if you have a larger cutter you will have to move it slower. The limiting factor is how fast the motor can cut wood.
Obviously if you use an extremely thin cutter your CNC machine won't be able to move fast enough, and if you use an extremely large cutter it will have difficulty accurately controlling the speed low enough, but over a broad range of cutter sizes it shouldn't much matter.
See also this question which also about efficiently removing wood with a router.