Any idea where the moisture is coming from? Deck hardware? Handrails?
I just went through this with the handrails along my cabin top.
I removed the handrails, drilled a larger hole where each screw hole was ( I think it was a 1/2 inch ) it was no larger than the base of the handrail, and no deeper than the headliner. I did the allen key in the drill thing and dug out all the wet balsa around the larger hole. Dug a little deeper around with an awl. Let everything dry out for about a week. ( we had a dry summer)
Then filled all the holes and voids with epoxy. Re-drilled new holes for the handrails and re-mounted/ bedded.
I think the important thing is to find the source of the leak. ( probably through some hardware ) You can probably live with some moisture in the core on the cabin top if it's not structural. If there's alot of water in there, it will freeze and thaw and cause cracking.
How old is the vessel?