I taped over the lower holes from the mounting screws and filled the void where the balsa was removed with West System epoxy thickened with 406 filler. I preceded this by covering the surface with straight un-thickened epoxy to get a better bond between the thickened epoxy and the surface of the void. I made the epoxy thick enough so it didn't ooze out. Once this set I drilled holes for new mounting screws. I did not drill through. I drilled and tapped the epoxy for 1" long 10-24 machine screws. That way there are no holes going all the way through the deck for fasteners and no way for them to leak.
I cleaned up the inner edge of the hole with a drum sander on my cordless drill and mounted the viewport with Boat Life Sealer Caulk (polysulfide like 3M 101). I wanted to replace the plastic in the view port but the threads to the collar that hold it in were in poor shape and getting it apart would probably have damaged it. That part didn't leak so I left it alone. If I can find a replacement viewpoint that matches the holes I can replace it. For now it is water tight.