Reducing wetted surface reduces drag (all things being equal).
Aero stability is a major concern. Having a huge vertical element like the airbox makes the car more sensitive to crosswinds, which is a bad thing. Some articles have mentioned making those cutouts to reduce such sensitivity. Don't forget that in 1938 Bernd Rosemeyer died in a land speed record attempt on the Autobahn when he expereinced crosswinds.
Indeed, however not only that but the rear cover effects the aerodynamics of the rear wing as well, hence desiging it properly can be a pain at times. In fact if you design a wing and test it in free stream, the results would vary when its on the car with all those body panels close to it etc, however the biggest changes are produced by the diffuser as well. This means that your wing design depends on your diffuser design as well, obviously no one like side winds. It should be noted that F1 cars are designed, aerodynamically speaking, for straightlines however Yaw up to 30 degress are also considered.
Furthermore, the 2008 regulations are quite exciting to look at. The turbulence produced by the wing can greatly effect the rear wing performance of the car, hence changing the pitching moment of the car, well it is quite hard to predict on how the rear covers may look like this time. One interesting point mentioned in the rules is the downforce is limited this time!
