how are they attached to the roof now? If it's a light bar that's clamped to the pinch weld / rain gutters you could possibly route a heat-shrinked pair of wires thru a door jamb with a minimum of exposure or ugliness. Even moreso if you can match the heat shrink color to the vehicle.
If you have any sort of factory roof rack you already have holes in the roof. It would be a straightforward thing to route the wires out of sight along the inner faces or even inside the roof rack itself and then down thru one of its mounting feet thru one of the existing bolt holes. Removing one of several mounting bolts somewhere in a trailing or middle position shouldn't lead to any problems.
lastly and 'properly' there are wiring housings that you will need to drill a hole for but which are designed to clamp together thru the hole and make any leaks nigh impossible. Typically used in the boating, RV and solar install world and I really can't think of the name of the variety of connector right now, been a long day. Someone in the 12v subforum should know the name. Maybe you can find a mod to move your topic there.
