If both tops and windows are up, I imagine that the heavier weight of the hard top would slightly hurt the MPG more during acceleration, same as the difference between the stock bumper and an aftermarket steel one.

 

I don' t think the weight of the tops effect it as much as drag that the tops create in configurations other than fully installed.

 

The hard-top weighs quite a bit, so I'd say that it would affect mileage (never really checked).

I notice that when I have my hard-top off, the jeep comes alive (as in bouncing around in the rear end more with the reduced weight and also in better, more punchy performance). Never been at highway speeds with no top (just around town & on the trails), so can't comment on economy there.

 

I concur with top-off losing 2-3 MPG.
If you really want to drop it, leave the back of the freedom top in place, but remove the fronts and all 4 doors. It feels like driving with a parachute.