I've come across a lockable cable design that seems to be the easiest answer.
You take two pieces of cable, make a large loop at one end of each and a very small one at the other. The large loops slip over, and down the bow and the stern of the yak, but are small enough not to reach the cockpit. You then join the two wires by the small loops with a padlock, under your roof rack bars. Once "locked in" the loops will not reach the ends of the bow or stern to release the yak.
I would suggest either wrapping the large wire loops with tape or rubber of some sort to minimize any hull abrasion.