uggested that roof racks should be used, only when they are very necessary or during the case of long travel.
Technically speaking, anything you install in the exterior of your vehicle is going to spoil the aerodynamic profile over the body. Installing a roof rack will increase the drag on the car, in the sense prove to be an obstruction to the air flowing over the body (As shown in the figure).

In order to overcome this, the engine has to produce an increased power, to move further, hence the fuel efficiency is effected,
Speaking of car's performance, aerodynamically it will be http://www.websolutionwinners.com/affected.
The only way to avoid this is to considerably drive at average speeds, the effects are minimal.
Also google about the cross winds effects, it will tell you why windows should be preferably closed while going on long drives for better efficiency.

for more info:

http://jpinds.com/
http://bigdaddymedia.co.uk/