Popping hooks is a very prevalent occurance. Much of what I've seen is caused by insufficient gluing surface on the hook and a hook design that does not adequately distribute the stresses over a large enough area. I've seen hooks designed that actually act as long armed levers - such a design is typified by a inadequately small gluing surface and a long hook that captures and holds the bungee at a distance that is too far from the hook/lid glue joint (long lever arm) - a hook designed like this is going to exert pressure that the glue joint can't handle (the epoxy doesn't stand a chance), especially when the kayak gets hot and the epoxy softens. Ideally the loaded bungee should be as close to the hook/lid joint as possible - this shortens the lever arm and lessens the pressure on the joint. If at all possible, reinforce your hook/lid joint with fiberglass to distribute those stresses more evenly. You may even opt to build a double-ended hook that spans the width of the lid. Not only does this distribute the stress over a much larger area but has the added benefit of stiffening your lid (some have had problems with warped lids). The same goes for the hull/padeye-hook joint.
This photo shows a lid with double-ended hooks.
Note also the central lid padeye - this acts as a tether/soft hinge.
Hope this helps.
Joe Redfish Kayaks