Ugh...hate roods, especially when they obscure a nicely-designed case.
But back to roof rails: you probably won't improve MPG by a clear or measurable amount. But removing the roof rack will still lower drag; anything sticking out above the body surface like that is responsible for interference drag--i.e. the drag added by the rails and crossbars is more than if they were moving through the air alone. Further, it's almost never the case that the airflow over a car is exactly parallel to the direction of the car's travel, where roof rails would have minimal effect. But any component of the airflow perpendicular to the rails will increase drag (because the sine of the angle of the car's direction relative to the sum of the wind velocity and vehicle velocity vectors is zero when they are the same direction [lateral component == 0] and != 0 when they aren't [ lateral component != 0]--which is most of the time out on the road).
So if you never use them, go ahead and remove them. It can only help.