I would think that since it is behind a wheel/tire and to a lesser degree, that they are underneath the car, the exposure to airflow is minimal. Not enough to really impact the actual mpg.
I'm guessing though...
I have a brand new OEM set I'd like to eventually put on my CRX. Got them off Ebay for $26. Take that! You money gouging dealership.
Stock Civic VX came with mudflaps all around. Aparently they're a hot commodity because I've had offers to take them off my hand. I eventually pulled them off myself and on a shelf in my shop they sit. I'll probably let them roll with the chassis when I sell it.