Here's what I did when I rebedded my stanctions on a boat I had some years ago...
Most boats do have wood cored decks. I took my power drill, put a finishing nail in the chuck with about 1/2" of the nail bent 90 degrees. Put the nail in all the holes and turned on the drill basically opening up the core and not making the holes in both layers of fiberglass any larger. After that, I filled the enlarged holes with epoxy. After that dried, I redrilled the holes. After remounting my stanctions, I knew if any water did leak thru, it would only come in contact with hardened epoxy and never soak into the wood core.
I did mine last year (the left side) and I'm going to do the right this year.
This is pretty much spot on, except that I overdrilled the holes first.
So the procedure I followed :
Remove core with nail
Countersink the top (and bottom if you can reach it)
Mask the bottom of the holes
Fill with epoxy
Drill correct hole for fasteners
Countersink the top of the hole (helps sealant do its job)
Assemble with butyl tape
Have a few spare bolts, nuts and washers (or replace them all) I had a couple that siezed or were badly corroded.
I filled with unthickened West epoxy, which will shrink a little when it sets so then you top off with some more. My deck is sloping, so the second batch of epoxy got colloidal silica additive to make it not run, and sit level with the deck.