At the kayak builder's day last Saturday here in CA, I saw a very good idea (patent pending, I hear)

The concept is to create a plastic U tube which the ends are glued into a block. The block is then glued to the back side of the deck. The bungee is passed through the tube and it is 100% water tight. I'm not sure how easy it is to thread the bungee through the tube, but what I saw looked very nice.

I've done the thing with only drilled holes through the deck and it leaks a lot. Don't do this.

Take care jim gabriel