Welcome to the world of Contessa's!
First, don't panic. Your boat is over 40 years old and has not yet fallen apart.
And apologies in advance for a long post.
The foredeck of my 1976 Contessa makes a crackly noise but is dry and otherwise sound. I have rebedded everything but the toerails on my boat which addressed any leaks due to absent and failed caulking. I have found damp plywood under the poop deck (adjacent to the transom) due to leaking and poorly installed engine vents. My firs suggestion to you might be to start looking at your boat in this area to learn how it is constructed.
Your boat predates mine and is an early example of how boat builder's experimented with using cores to make their boats lighter. For modern boats, the inner and outer skins are similar in thickness, just like the top and bottom of a steel I-beam. This takes the best advantage of using cores (whether wood, balsa or foam) to lighten a panel. In the case of our Contessa's plywood was used as the core (or the web of an i-beam) -- it is heavier than balsa but was commonly available and familiar to builders who were migrating from wooden boats to frozen snot fibreglass.
If you lift out one of the clamshell vents you will see that your deck is a sandwich comprised of gelcoat, between 1/4" and 3/8" of solid glass and resin, 1/2" to 3/4" of plywood and finally another skin of fibreglass which might be as much as 1/16" thick. There are photos showing this style of construction in the gallery.
Also note that the plywood may not be fully encapsulated -- mine was not. The builders laid a tow of wet glass over the plywood but left two of the four plywood edges exposed. The good news is that in this configuration the plywood will dry itself out once you address how the water got there in the first place. If you want to see another part of your boat, try lying on your back in the foot-well portion of your quarterberths. There is no liner here and you should be looking up at the bottom of the winches and the reinforcements for the side decks. The point to understand here is that the builder used the plywood to stiffen a spongy-feeling deck but the strength came mostly from the fibreglass and not the combination of glass and core. For the most part, the bottom flange of the i-beam was never made so the real strength in the deck remains in the upper fibreglass layer. Fibreglass is a plastic composite -- it is EXPECTED to flex -- so again, don't panic.
The crackle in the foredeck on my boat is an old problem and may go right back to the original construction of the boat. It is not uncommon for boat builders to fail to use sufficient resin in layups and this leads to dryspots. Wood and balsa commonly soak up resin like sponges and make leave the boundary between the core and the adjacent glass dry before the resin kicks off. Also, remember that the core that Taylor's used for our boats was plywood. In larger panels such as a cabin top, there may be a void between the flat plywood and the cambered deck.
Next step: one area I would look at would be the condition of the mast step. It is a poor design IMO and directs water into itself. You should get a moisture meter and compare its
state to the rest of the boat. You can learn a lot about your boat from a moisture meter and a few holes drilled upwards from inside the boat. Also, follow your nose -- does the boat smell rotten -- moldy or mildew? Do you see water streaks or leaks inside the cabin? If not, then your deck may not be too bad.
The liner is just that -- a liner. It is a skin which is loosely attached in a few places inside the cabin. It is intended to hide the rough underside of the deck and reduce condensation. In your Contessa it is not structural.
Something else: rotten deck cores are a very common problem in all boats and there are many ways to make the repair. Although I am in Canada, I have worked in the boat repair business and I would be shocked if a deck re-core for boat this size would cost more than $5k. And you can help the shipwright along the way by removing and reinstalling various fittings (you'll be trading off epoxy rashes for days of 4200 stickiness but you will save a lot of labour as well as learn more about your boat).
Finally, my advice is the same as Seeadler's: go go sailing. The boat is great funm and even with a creaky deck it will be a pleasure to sail. As you learn more about the boat you can decide what repair projects to tackle.