Like most things (bikes, boards, skis, etc), I think a lock for your boat is a deterrent. The more intimidating you make your security look, the less attractive it will seem to a would-be thief.
I use a cable about the size of my pinky finger & pass it through as many holes on the boat & rack that I can find (security loop to seat to rack to basket on rack to bike rack and so on). When I travel & end up leaving my boats on top of my car in front of a road-side hotel, I use 2 separate cables & locks: one on the front & one on the back.
The bottom line is that some people are just dicks. They will take your stuff no matter how much thought you put into securing it. For those people, we have bottomless cliffs, avalanches, strainers, undercuts, poisonous snakes/spiders/scorpions, and all sorts of other stuff that karma uses to balance everything out.