I think the ports fail because the deck in that area continues to flex.
From an engineering standpoint, ports weaken your hull. Fiberglass Hobies hulls are constructed with a fiberglass-foam-fiberglass sandwich, which in engineering is a structural beam- the foam is called the web and serves to keep the skins apart- the same principle as in airplane wings- two skins held apart by ribs. A port removes skins in an area and replaces them with a weaker single skin (plastic port) and so creates a weaker and more flexible area.
Now if you want to add ports to a delaminated hull and end up with something that is actually stronger but not much heavier than the original, here is what I would do.
1. First locate, size, and cut the port openings.
2. Carefully remove 1 1/2" more of the inner fiberglass skin from around the hole on the underside of the deck. A Dremel-like tool with small circular blade works well. It is ok to cut into the foam, but do not cut into the outer skin.
3. Use sandpaper to transition the foam back so it is totally removed from the first 3/4" of the backside of the outer skin from the edge of the hole then slope it to the inner skin. Roughen and clean the 3/4" of exposed outer skin
4. Next join the inner skin to the outer skin by laminating 3 or more layers of glass to the underside of the deck starting at the holes and going outward across the tapered foam, and up on to the inner skin a couple of inches past the delaminated areas. Make sure you roughen and clean the old glassed area first. It may be easier to make a hole in the glass fabric that is slightly larger than your hand then wetting out the glass and doing the lamination on a sheet of plastic wrap- it is easier to apply and squeegy off excess resin that way. After wetting the inside/underside of the deck lightly with resin you can cut a hole in the plastic wrap, put the complete lamination in place on the bottom side of the deck, brush/stipple or roll it down, then remove the plastic wrap. Don't worry if the glass extends into the hole opening, it can be trimmed later. (hull will need to be upside down.) (If the deck were flat a plywood or micarta stiffener could be used under the outer skin)
5. Make templates that mirror the cross hull profile of the underside of the deck just forward and aft of the holes (outside the tapered area)
6. Make four (two for each port) 2" - 3" wide deck beams from 1/4" - 3/8" marine ply or rigid foam. Round the edges of the beam that will be away from the deck so you can wrap and laminate multiple layers of glass on it - lay glass fiber on the bias (diagonally to) the edges.
7. Put "peel ply"* on both sides of the laminated beams (*after the resin has cured and peel ply is peeled off it leaves a rough surface ready for further glassing or attachment) or once the beams have cured roughen the layup on the beam faces with sandpaper.
8. Re-check and adjust the fit of the beams if necessary to make sure they still match the underside of the deck.
9. Combine fiberfill and resin to a THICK, peanut butter consistency and bed the beams in it to the underside of the deck
10. Use extra filler to make a nice transition radius between the beam and the under side of the deck, then laminate a couple of layers of glass (on the bias) to attach the beams to the underside of the deck.
11. Once everything has cured and the inner skin is rigid and reinforced you can repair the delamination by drilling holes in the outer skin and injecting resin as describe elsewhere here. When that is done, install the ports. You will have a deck that is stronger than the original.
These techniques are used building fiberglass composite aircraft and result in a
VERY strong structure.
If you want any more detail about these techniques search composite aircraft building or the Experimental Aircraft Association.