Denatured alcohol works pretty well at drying out the wood, since it will combine with the water and then evaporate.
How extensive the rot is may depend on the core. If it's plywood, the water will migrate with the grain in all directions pretty quick, so if you open it up, you may find a lot of rot. If it's end grain balsa core, water migrates much slower across the grain, so the rot may be limited to a smaller area. If it's the original deck, it may be balsa core, although my boat has plywood in the area of the seats, so they may have used plywood to handle the higher loads of the engine box hinges. Island Trader's suggestion will give you an idea of how extensive the rot is.
If the area is not real large, it's probably worth drilling a series of small (~3/16") holes in the rotted area and injecting some alcohol to try to dry it out. Once it's dry, you can inject Git-Rot in the holes to saturate the core and stiffen it. However in the area of the hinge screw holes, I'd want to drill them out (top skin only; try to avoid going through bottom layer of glass!) with maybe a 1/2-5/8" drill the then use a bent nail in a drill to remove whatever core is left over an area of a couple inches in diameter. You can then buy empty caulking gun tubes, put some thickened epoxy in 'em, and use a caulk gun to inject the mixture into the area you hallowed out. I would then drill and tap the cured epoxy for machine screws to mount the hinges; they'll hold better than tapping screws, especially if you put some blue locktite or 5200 on them!
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