This takes a little explaination-I happen to be one of the owners who had core problems. This needs to be put in prospective. I recently purchased an "AS IS, WHERE IS" 2003 C Dory 25. I was aware of a bad survey--but I paid less than half of the value of the boat. What had happened, is that the cockpit floor was made of 1" balsa core. There are two cut outs for about 12" x 20" hatches and two 6" round inspection plates. These hatches were put in with silicone sealer; there was no attempt to seal the edge of the cutouts by the factory or the first owner (who was very nieve about boat maintance). At some point a "friend" jumped into the cockpit of this boat, and cracked the deck--the boat was covered under warantee, but the owner didn't contact the dealer or factory. (There may have been reasons to not have confidence in the dealer). There was also a question about the transom--at survey. The factory was contacted about that, and would have paid to repair it. The reason the cockpit deck cracked is that the top layer was only 3/4oz mat, with fairly thick gelcoat with additional Cabosil added to allow texturing with a roller. There was already rot in the deck core when it was jumped on. I do know that the boat was left open during at least two winters in New Jersy. Water and snow stood in the cockpit and moisture got into the core of the cockpit. This accellerated the deck core rot-and water intrusion into the deck core.
We cut out the entire bad area of the deck, (about 30"x width of the cockpit) and put in 1" Nida-core (this is a poly prop/fiberglass mat composit hex cell hollow core material). We used the 3/4 oz mat and 18 oz roving bottom layer, plus another 3/4oz layer on the bottom, the Nida-core and then 3/4oz matt, plus 12 oz bi-axial material with polyester to laminate an entire new deck (also covering the old good balsa core). There were also a number of screws into the top of the bottom of the hull--(cored with one inch of balsa). One of these screws had some moisture in the core around it. All of the screws in the hull were removed. In a few circumstances, an epoxy core was inserted and a screw re-inserted (like in bilge pumps screwed to the bottom of the hull). The other screw's holes were drilled out, undercut and the core filled with epoxy filler. The screws were replaced with fiberglass tabs, to hold the "furniture" in place. (with a fillet between the cabnet and the bottom of the hull). We rebuilt part of the transom--although there were two cracks in the splash well, and into the hull to deck joint on the top of the transom--there was no water intrustion into the core of the transom. (We took test drillings, did find a void at the bottom, where the balsa was not continued under the wood core of the transom--and filled this with glass and epoxy.) I spent about 10 full days and a gal I had working for me also spent about 12 days working on the boat--and it is better than new.
C Dory has been using cored bottom of the hull for about 30 years. There have been no known failures of these hull bottoms, including boats falling off trailers, rear ended, and thrown on jetties near the Columbia bar (all of these boats were rebuit and are used today). One boat was recently cut in half and extended 2 feet, using balsa core! A pretty good record!
The reason that C Dory uses Balsa core is that the boats have a semidory bottom--basically flat. Solid glass would be prohibitly heavy--the boats are light and thus perform well. The key is that there is plenty of glass over and under the core. AND--you never put a hole in the core! (the company changed hands--and I guess this mantra was not passed on.) They know this now--and the company has stood behind the repairs we did, despite a "non transferiable" 5 year hull warantee. I am aware of at least one other minor core problem--same cause.
There are a number of core materials--any of the woods are subject water intrusion. However, any of the synthetic can also have problems, such as core break down. Wood is still an excellent material--BUT we have to know how to protect it. In our project of looking at cored boats with ultrasound, we cut up 20 cored boats (hurricane damaged) and core delamination was extremely rare (basically non existant)--even boats which had fracture of the hull and water intrusion from the hurricane damage.