I don’t think the vortex generators will provide much benefit if you have the rack on as the rack will already shift any laminar flow to turbulent flow with the rack itself. Turbulent flow is able to “handle” bigger flow change gradients than laminar flow. That’s why they put them on the rear of cars. They reduce the suction drag by letting the turbulent air roll down the back better than laminar flow. Same reason they put retractable vortex generators on the leading edges of wings so at high angles of attack, when laminar flow would separate and cause a stall condition, the turbulent flow follows and still provides lift.
I think a deflector mounted on the rear of the rack to pull some air down the back window would be more effective than the vortex generators. At the end of the day, you have a vehicle that has a large frontal area with a lot of drag points so unless you put a fully contoured faring over the rack to provide a clean top surface, there is not much to gain.
I would hazard a bet that if the roof rack had solid sides instead of bars, you might see an improvement as well, when it’s empty. The solid sides will allow a zone, or balloon, of turbulent air to be created within the rack providing a sort of buffer for the air coming over the windshield and act as sort of invisible faring and minimizing the drag caused by air hitting the bars.
