Hello Newbie3,
Since no screw heads are visible around the other sides of the hatch opening I would guess that a repair occurred in that area from the underside of the deck. Anything from loose trim, replaced hatch, to removed core material due to a leak could be reasons for the oddity. None of those reasons are earth shaking. Investigation (if there are no other screws) could include removing those three screws and "seeing what shakes out". Alternatively, if there is no leaking and no unusual bends or cracks on deck, just enjoy sailing the boat.