I will give you my most likely scenario: First I don't believe that any of these are structural. The ones on the cabin meeting the deck, is an area which is a fairly sharp area in the mold. (remember the mold is reverse of what you see). The first item sprayed into the mold is the gel coat, then an opaque layer (in this case blue gelcoat). It will be thick in these inner recesses. The next layer is mat to keep roving from printing thru--but the mat is sort of "stuffed" down into this rounded area--and occasionally there are minimal voids there--little air bubbles, which may not be "worked out'. On top of that are several layers of 24 oz mat and 3/4 oz roving--alternately for this specific boat. The roving is where the structural strength is.
Inside the hull to deck joint is an "edge to edge" match. The hull was kept in the mold, and then the deck was placed on top of it. When lined up just right, some tabs of glass were set between the deck mold (including the cabin sides and cockpit gunnel sides) and the hull. Then the entire seam between the hull and deck were glassed together from the inside. What you are seeing at the upper edge inside the V Berth, just under the deck, is a little edge of one of those mat layers. Again, nothing structural there. The real structure is in the mat and roving which made the hull and the deck. The little dabs are the inside of the rivets which hold the cosmetic rub rail extrusion ion place. They are ground close to smooth, and then covered with a dab of...depennded on the year and factory--anything from epoxy, polyester paste, to Bostec sealant...maybe some other item.s. This is just cosmetic.
Now--I cannot tell about the rest of the V berth because it needs a good cleaning--if the tabbing which holds the V. berth in place is broken free from the hull, it may mean the boat was driven very hard, pounding...again not a danger, but something which should be addressed, with a new tabbing, using epoxy and cloth.after the area is cleaned, dried and then lightly ground to a good glass surface. I am not saying that this boat has been abused--because I cannot see that area well enough with the amount of mold or dirt (this is easily cleaned with some bleach, soap and water, plus a hose rinse. A beauty of the spartan interior of the C Dory.