I have had the factory crossbars on my CX-5 for a few months. They are very easy to install and remove (no tools needed to remove and reinstall), so if you notice any negative noise or mpg effects, you can store them when they are not in use.
As long as they are moved all the way back when not in use (as suggested in the instructions) I do not notice any extra noise. If the front crossbar is in the forward position I did notice some low frequency humming at ~40MPH, so I moved the crossbar back to where it should be when not in use and the humming was gone.
I do not think the crossbars have any measurable effect on MPG. The definetly do not help, but I do not think they hurt much either.
Please do not try this, but imagine holding one of the crossbars out the window of the car traveling on the freeway. The crossbar is so thin that the ammout of drag generated by it will be very small and will not slow the car much.