I shell will add more drag than just the standard bed. Adding the large drop and flat surface on the back causes more air disturbance and drag, it makes more "dirty air".
Mythbusters (everyones favorite, I know) did a show about this very thing and found that the open bed will actually trap air inside creating a bubble of high pressure forcing all new air to flow from the top of the cab out over the tail gate and not into the tailgate. You still get the swirling effect from the cab itself but not all the way to the bed floor. Thats why stuff doesnt just fly out of your bed as you drive around, but if you open your rear slider you will get some stuff flying into the cabin.