Air resistance is the main culprit in mileage loss with a roof rack. A really heavy rack weighs less then a person, and your mileage doesn't vary noticeably when by adding a passenger, does it?
Air drag goes up at the square of velocity, or in English, double your speed, quadruple your drag. Our bricks have pretty high drag to begin with. Add monkey bars to the top, and it goes up even further. Add 4 cup saucers(lights)or pie plates(big lights)and you might be able to add a full point to your base drag coefficient.
If you want to make a low drag rack, figure out a way to press the tubes into an oval, and orient the long axis front to back. Oval tube has about 2/3s the drag of similar sized round tube.
As for the stock cross bars, I was wondering about that myself. I'm making a long highway trip next month and was planning to pull them off and see if it made any difference.