The warping and staining is a clear sign of prolonged water intrusion - not good but not necessarily fatal, and with a good seal the damaged material should be replaceable/repairable.
The cracking, if due to a "mast stepping incident" should be investigated further, first by getting more detail. It's also possible that the deck stay was not taking the halyard loads properly, and that the stress on the deck has come from there. The deck stay is there to counter the tendency of tensioned (led aft) halyards to lift the deck.
There are a number of ways to get a good seal at the partners, various boots are available, cloth(sunbrella) boots can work, and pourable compounds like "spartite" also are used to seal the gap and locate the mast in the hole.
With luck you're just looking at cleaning up or replacing some damaged plywood/veneer.
1984 Fast/Nicholson 345 "FastForward"
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)