During the build of my cedar strip kayak, I cut out the hatch prior to mating the deck and the hull. During the process the deck is now flatter then the hatch cover. Because of this I can not use my original idea for securing the cover. The interior shock cord. The hatch won't sit flat enough for a seal. So, I figured I would have to use exteror straps.

You can probably 'flatten' the hatch cover to get it to match the deck, if you want.
Removing the glass from the inside of the hatch lid usually makes it a lot more flexible. Then you can re-glass (and even add stiffening 'beams' to) the inside of the hatch lid with the correct curvature.

Even with exterior straps I think you'll have problems getting a good seal if the lid and hatch recess don't fit closely without pressure.