I suppose each affect cd in a very small way. I would guess that you might burn an extra gallon or 2 of diesel over the car's lifetime. If they really do help much in preserving the paint job, you would have to be an absolute morooon to remove them for anything other than cosmetic reasons.
As for the roof. It is already a pretty turbulent area. It is a low pressure area so tilting the roof open is a very good way of sucking old air out of the car while drawing new air in through the vents. If the airflow was high enough. It might even work to smooth out the turbulent low pressure area, resulting in a reduced drag. I doubt this is the case, though. I think the worst case is, you have a slight raise in drag over a vehicle with all windows closed.
Problem is if the outside temp is much above 50-70 degrees (dependent on sunshine level), you will want either a window open or the A/C running. If you have to open a window, I find the sunroof open a lot quieter than a window. And it certainly is more efficient than the A/C.
