I broke a beam bolt and had to access the aluminum block under the beam; ergo a new port in back of the front beam. Also broke a shroud chainplate (thunderstorm flying across a parking lot) and had to access the nuts on the inside of the hull; ergo a hatch behind the daggerboards. I felt more comfortable doing strong but rough work on the top deck than I did messing up my bottom. In both cases, I sealed the foam around the cutout, and installed circular backing plates under the ports inside the hulls. I also picked the smallest possible ports I could fit my hand through, and looked for sturdy ones. I haven't seen any issues. My ports are FAR superior to the stock aft ports, IMO. I will grant the boat looks ghetto
I had previously installed a big storage port, but made a dam and bedded that in thickened epoxy to provide a flat surface on the curved deck. With the epoxy and backing plates, I still think that's the strongest part of the deck. Not sure I would do this again, but with a fat bag under it, it did provide good semi-dry storage. Not totally dry, but The boat could sit upside all day and not leak a pint. I can live with that. In your case, I would agree to pull 'em off and glass over.