No, its not too high for roof racks. I have just installed both fan hatch and racks (both purchased from CLC). There is however only 3/8″ -1/2″ clearance between the center of the hatch and a straight line between the tops of the load bars. If a kayak is dead center over the hatch, the hatch needs to stay closed. Alternatively if one has kayaks on Autoloaders (on their side, one each side, for example) the hatch should be more functional without removing kayaks.