I have a balsa core old C&C from the '70s. There is no headliner to speak of and where there is no paint (beneath the minimal headliner around the companionway hatch and in the forepeak), you can see the results of water intrusion into the core.
I have rebedded and recored virtually every piece of deck hardware. I have done actual core replacements (with encapsulated marine plywood) under the entire port genoa track, which ripped right out of the deck at one point during a blow. No, neither I nor my guests were amused with a car and block flailing at high speed as I tried to tack over to ease the sheet.
Consequently, I "drill and fill" exactly as is listed in the works of Saint Don Casey. It's a two-day job, but can take as little as 15 minutes per day per deck fixture. I grub out the old core (the messiest bit) with a small Allen key on a Dremel, or even just by hand). Then I run a hairdryer on the area to evaporate and further "honeycomb" the remaining dead core, which is only a matrix for fresh epoxy at this point. Then I tape over the hole from the bottom fill it with an epoxy slurry, and (here's the refinement) brace a flat plate of something wood or plastic from below and put some sort of metal weight above, compressing the glass layers and the setting epoxy. Cover and let harden. Drill out the next day (with heed to temperature, etc.)
A further refinement is that I put a spiral of caulk on the SS through bolt around the mid section. As the bolt goes in, the caulk seals the threads and makes a very neat and minimal "doughnut" as it seats in the cleat, winch base, whatever. This takes a little practice to gauge the correct amount of caulk, but it isn't much. I rarely have to wipe or Exacto-knife any surplus off.
Lastly, I cut 1/4" aluminum backing plates to spread the load beneath. I will put a fine bead of caulk on the topside of this plate, and I will torque down the bolts in two stages: finger-tight on Day 1 and then to final torque of maybe 35-40 ft/lbs. on Day 2. Having a helper with a screwdriver is handy here.
I end up with revitalized and strengthen core that resists water at the hole, at the caulked bolt threads and at the beaded backing plate, which spreads the load and mitigates the core damage. It's not as good as REPLACING the entire damaged core area, of course, but if I did that, I'd never go sailing!
My boat passed survey better in 2007 than in 1999. It is 34 years old.