If when you remove the portlights/hatches you find exposed core as I'm sure you will it needs to be replaced with thickened epoxy. If you don't a future leak will not be visible as it would go directly into the core. The solution is to remove the core all around the cutout as well as around the fastener holes. Fill it with thickened epoxy and then redrill the fastener holes. This way you will see a leak inside the boat and can attend to it rather than it just rotting the core. With any luck there will not be any core damage already present. Here's a link to an excellent how-to for potting holes for fasteners.
Sealing Deck Penetrations to Prevent Core Rot Photo Gallery by Compass Marine at pbase.com