I had a similar issue. I had a bad caulking where the top and bottom of the hull meet. I had to remove the rub rail to seal it. It only leaked whenever we were getting up on plane. I’m sure it was from a rough day when the boat was flexing against a docking pile. The seal just split. 5200 fast cure took care of it.
maybe , my hatch was leaking BUT the water was running under the headliner .( water finds its one route) so i un screwed the hatch both sides and it pops out . look at core between the fiberglass if its soft and mushy thats were your leak is . dig out the mush and fill it with piece of solid wood (its easy ) fill it with silcone re bed the hatch and that should do it