The reails weren't fitted on most later DIs in the UK, and it looked better without them. Of course, there's a difference between not fitting them in the first place and removing them from a vehicle that already has them - you'd need to bung the fixing holes and could find paint or corrosion issues under the rail feet. If I had them, I'd probably just keep them.
As for the drag of high or low roof racks, the rack is going to be the same height at the rear regardless, so any effect would just be from trapping air in a funnel effect at the front of a level rack, which might be reduced with a stepped rack, but if the rack is not boarded, such an effect would be very small. That step isn't going to help those with sun roofs, though...
