kenwood make 6 inch subs...not a bad idea if you want a little more bass and have no room...so i wouldnt bother. 8 inch subs are available aswell, but depending on the type of bass u want (if you want it to sound half decent) i wouldnt bother putting them in the shelf...but if you must, "free air" subs are made for the shelf. but a word of warning...the back shelf plays a part in "safety" with the car in a collision, infact, the whole car is designed to disperse the impact evenly, so if you go cutting out bits and pieces here and there, you could be causing problems. and your car mightnt be roadworthy.
if you want a lot of bass inside the car, you can get a box made up that ports through the shelf...smaller holes and looks neater, and more inconspicuous