I've got mixed feelings about deck lines. All those pieces of string running around the deck mess up the beauty of the wood, but if you should end up swimming next to the boat for some reason, having something to grab onto may save your life. I am even more ambivalent about hatch hold-down systems. Again, most systems mess up the lines of the boat, yet hatches are really useful for carrying gear. Hatches need to be very reliable, yet not interfere with the useful storage volume inside the boat. I am experimenting with magnetic hatch hold-downs (a-la Rob Mack's of Laughing Loon), but I continue to harbor doubts about their reliability in the harshest conditions, so I'm going to put shock cord straps over the hatch under the belts-and-suspenders principle.
So, I'm going with some deck lines. I'll have a basic shock cord system in front of the cockpit and some more around the hatches. I want to keep these as low profile as possible. The system I've determined to have the least visual impact is a simple hole through the boat with shock cord pulled through the hole.
If you make a 1/4" hole and pull through a 5/16" shock cord, the cord will pretty much seal up the hole with maybe a little water wicking through the braided jacket of the cord.
Whle this is very simple, a hole in the shell of the boat introduces a way for water to get into the wood strips. The simplest solution would be to drill an oversize hole, fill it with epoxy and then drill the final hole.
I decided to do something that looks a little fancier. I'm using a maple insert to make the hole. Maple has closed grain that does not absorb water and being harder is more durable than the cedar strips.
Making the Feed-Through Fittings
I start with a block of wood and some router jigs. I've got the jib set up to make two fittings per side. The wood is thick enough that I can make fittings on both sides. The jig defines the outer perimeter of the fitting. Using a plunge router I cut the outer shape to a depth slightly more than the thickness of the kayak deck. I then use a countersink bit to create what will become a chamfer at the top of the hole. Then comes the hole itself. Since I was making fittings on both sides of the block, I used the tablesaw to cut the block in half. At the bandsaw the outer perimeter of the router groove defines the cut line. I then spend time at the belt sander cleaning up the part of the fitting that will be inside the boat.
The same jig that was used to router the fitting in the block is now used to cut the hole in the boat. I include a collar on the router bushing to account for the diameter of the router bit.
The fittings are installed by pushing them through the hole from the inside and are held in place with thickened epoxy. After sanding the excess off the outside they will be protected by a layer of fiberglass inside and out.
Mariner Kayaks has been doing something similar for years and has a good FAQ about getting shock cord through the hole.