It depends on where you're going, what the hatch material is and how long you want it in there. "Sealant" is generally thought to provide waterproofing, whereas caulk/bedding is meant to seal the barrier between some sort of rubber gasket stripping, the window and the frame.
I can get away on my old boat with silicone and gasketing, which conforms closely to the frame and leaves the silicone to do an essentially finishing seal. The new boat is an oceanic cruiser (or will be) and is 1/2 inch through bolted Lexan with what looks like a further 1/4" of sealant...it's hard..but you can mark it with your fingernail...and the fixed portlights don't leak. The pilothouse overhead one have auto-type compressible gasketing (rubber to rubber, soft) and they are beginning to fail.
Some pictures of the hatch type would help. I would bed the hatch frames themselves in something like 4200 or 291 caulk, dog down lightly on the bolts (which I would individually bed with caulk and back with thick fender washers inside), and then the portlights themselves would depend on location and material. Foredeck hatches will see more water and UV than something on the cabin sides, for instance.