I have flush/invisible hatches on my kayaks. I've used different seals over the years, but never the standard kit smooth black foam seals. Seals might need renewal every few years, and I always store my kayaks with the hatch hold down pressure released so as to prevent permanant compression of the seal.

If you go to Ace or a big box home store you'll find many options for seal/gasket materials.  What you choose will be dependent upon the exact clearances of your hatches and where you place the gasket.  Get a good feel for the height, width and resilience that will work best, and consider the amount of hold down pressure your set up produces.  Then choose accordingly from available options. The one that seems to have worked best for me is a white, foamy-but-rubbery material that has a generally square (1/4 inch sides/top/bottom) cross section and has some slight ribs on the top sealing surface. I'm not sure where I got it, or if I could find some again if I went looking. 

If you do go looking (including looking at various stores) you'll find many options, and several probably better than the standard black foam rubber. I also think it best to stick the seal to the kayak, not the hatch, thus forcing water to go up-and-over to enter the compartment - not allowing water to sneek under any area of imperfect seal contact. I don't stick the seal on top of the wooden ridge that is on the kayak-side surface under the hatch, but just outside it in the drain channel, and then try achieve enough hold down pressure to bring, or nearly bring, the hatch firmly down on the wooden lip when the gasket is compressed. I do try to be sure to still leave a clear drainage channel around the outside of the gasket under the lip of the hatch, as per the design/plans. 

I recommend Silicone Rubber Seals. Silicone is highly resistant to aging, UV rays, and temperature changes, which is essential for marine applications. A silicone rubber seal will offer a long-lasting, watertight seal, especially in harsher climates.

Buckshot Roulette