This is a common issue with all wooden anythings. It is due to the timber expanding and contracting from winter to summer, rain to shine, jupiter aligning with mars and so on. It doesn't matter what you put down the gap, more epoxy
what have you, the problem will continue. You actually have to creat an expansion joint if you want to do the job correctly.
Firstly, you have to ensure the hatch
joints are well fastend. No good in doing any of this if the hatch
is actually falling apart. If it is falling apart, then total deconstruction and reassembly is required.
But assuming it is in good condition, take a router of some means of actually channeling a notch along the seam. You need to go at least a 1/4" deep and the same wide, deeper if you can, but no wider. Now fill the channel with a good adhesive
sealant. Sikaflex is a good choice. Only because it has primers available to ensure you get a very good adherance to the timber.
This joint will now act as an expansion joint. It doesn't matter how much the timber moves, the joint will expand with it.