It appears to me the main drag would be the wind coming over the hood and up the windshield and directed into the boat where it then hits the transom sitting right above the roof with not much escape. You might try a cover but I don't know how long it would last. Or raise the back of the boat up 8-10 inches. That would make the top(bottom)of the boat like an air dam for the trailer and give a larger area for the wind under it to escape and easier since the transom would be at an angle.
Another thought, maybe put the kayak under the boat. Less drag and helps fill that void. Hmmm boat seats could be a problem.
Have fun...