The racks are typically spaced 3 feet apart which is too close together for objects that are 16’-18’ long. (3 foot spacing is ideal for bike rack and mounting skis.) Also, Kayaks have a big surface area which can pick up a lot of wind loads that will be transferred directly to the rack. The long overhang at both ends of the rack can result in cantilevered forces that can readily overload the racks, even if it’s just for a split second.
I would suggest making the kayaks as light as feasible. I.e. store as little as possible in the compartments. If you have to store items in the compartments then put them in the cockpit as suggested above.