I drove bikes thousands of miles on the roof of our last car – most of the 35000 miles we drove in it over 5 years were with bikes on the roof. We also had a Thule wheel support tow bar rack which only got used when two bikes were already on the roof.
In my experience –
– I didn’t notice any problems with headsets or other bearings on roof racks. It’s probably worth giving the bikes a bounce on the back wheel when you get home if it’s wet but beyond that I’d not worry. Up on the roof they’re actually out of the worst of road dirt and spray – in wet weather they come up fairly clean BUT not as clean as something that’s been jetwashed (ie that’s far worse for your bike).
– on the back, in wet weather, all the crap off the road gets sucked up onto the bikes and they end up covered in road filth. That’s when they end up really salty in winter.
Roof rack hits fuel economy by about 20% – we got c40 out of a Golf TDi whereas you’d hope for closer to 50. I’d be surprised if a rear rack didn’t have some impact anyway.