Dan,
I'm pretty sure there is plywood sandwiched between the cockpit sole and the headliner in the aft cabin. Not sure about the exact thickness, but I would guess somewhere in the 1/2" range. You can get an exact idea of what is in there by taking the cover off the steering gear in the aft cabin. The steering cables turn around pulleys and go aft to the quadrant. If you look near the pulleys you should be able to see a cross-section of the cockpit sole. I suppose it's possible to have moisture delamination in the cockpit sole, but other than the area around the pedestal, it would be hard to see how. Maybe borrow or buy a moisture meter and check the underside of the sole? Other than people jumping into the cockpit, that really isn't a highly stressed area. Possibly there is a void in the fiberglass/plywood sandwich? I don't think it's a big deal, but it's hard to tell for sure without seeing it in person. Hope this helps.

I was sort of thinking the same thing, a delamination. My first boat, an old Watkins 27, had some areas on the foredeck where the fiberglass had separated from the plywood core. There were no fittings anywhere nearby, so unlikely that it was due to water intrusion; which would seem to also be a remote possibility for your cockpit sole. I attributed it to a poor bond when the boat was laid up. I never repaired my old boat (traded it for a new C30), but that 'soft' feel always bothered me. I think Tom is on the right track for how to diagnose and repair.

Some models / years have a window in the cockpit wall above the aft cabin. Some owners have added these to the older boats also. If this is not bedded properly water can get in and run down the inside of the cockpit wall and then sit and seep into the plywood core of the cockpit floor and rot it. This is not uncommon on other types of boats, I haven't seen it on a Catalina 36 yet but doesn't mean it doesn't happen.

Certainly the area where the steering cable bracket is bolted through my cockpit floor has been damaged in the past by moisture.

I would say the plywood is probably 1/2" as well. It could be more.

Prior to purchasing my boat I looked at an earlier model that had been raced quite a bit, the cockpit floor was very spongy. I assumed it was from to many deck gorillas jumping on it. The broker claimed it to be an easy fix of some epoxy injection, not sure if that took care of the problem long term. I passed on the boat for this and other reasons. I have seen the boat several times since and didn't see anyone falling through the cockpit.

well, i got to replace my entire cockpit floor thanks to the PO and i can tell you that the floor is composed of 3/8 marine ply with layers of mat, roven woving and at least some cloth. the problem I encountered started with me removing the pedestal to get it powder coated. I noticed that that the core was wet enough around the pedestal that I removed some of the floor and kept removing it till there was basically none left. I wound up replacing the whole area with 1/2 plywood and several layer of fiberglass until i built it up to around 1" thick. I used epoxy because i was more comfortable using it but if you can fiberglass it would be alot cheaper and faster as it sets up quicker than epoxy. it is not an easy job but it can be done. I have pictures if you want to post a private note i can forward then on to you and I did have a write up from Catalina on the layup schedule for a Mark I but i haven't been able to locate it since i have changed pc's since then but you should be able to get the info from them. the problem i saw was once the moisture was in the core there was no where for it to go and it must have had a leak for a long time as the wood was MUSH for almost the entire length of the floor. oh yea I guess i should thank the surveyor that inspected the boat as well.