Simply adding a porthole to the area is not a good idea. Portholes are no where near as strong as a properly laminated composite sandwitch. Just adding a porthole will allow the soft spot to continue to grow.
If it were me, first thing I would do would be to inject resin. If the deck is delaminated, then regardless of what other repair methods are used, it needs to be re-laminated. So start by doing the injection.
If the deck is still soft after injecting, then likely one of the fiberglass skins has fractured. The skin would then need to be reinforced either with additional glass, or by also adding bulkheads as described in the article. You could access the inside of the hull either through the bottom of the hull, as described in the article, or by adding a porthole (only after injecting resin).
There are a couple advantages by going through the bottom of the hull. First is that you don't have to re-build the sandwich layup when you patch over the hull since the bottom of the hulls are solid fiberglass. You also don't have to deal with repairing non-skid. The second big advantage is that your access hole is on the opposite side of the hull from where you're doing your repair. This means you don't have to reach around 180 degrees to try to work or to see what you're doing. Working inside the confied space of a Hobie hull can be very difficult.
The only problem with doing that - where he's got the problem - is you've got a big block of styrofoam in your way (the flotation block).