Unfortunately as a first time post photos can't be uploaded as far as I recall - need 25 or more posts I think.
Photo 4 in the 12 below shows a plastic deadeye on the front of the cabin as alluded to by Lydia for kite pole downhaul - would the holes you are referring to be where this used to be?
boats-from-au.com/not-specified/endeavour-24-mkii-208733/208737A few cup fulls of freshwater would be unexpected but the holes should have been well filled with at least polyester filler (epoxy better) and satin white polyurethane 2 pack paint neatly applied over the top. So where was the water coming from? Presumably voids in the silicone and then it got into the headliner of the cabin front deck head if such a headliner is fitted? Don't believe these E24s had end grain balsa sandwich decks but if so there would probably be the source of the water - need to dry it all out and syringe epoxy resin in to re-glue the end grain to the skins. And hope the de-lamination is not too large an area. Tapping the glass skins with small hammer will indicate if any voids are there.
The hatch should have drain holes / tubes but the 12 photos at the above link don't seem to show any. These drains should be easy to find and cleared with a wire poked back up them.