The carpet won't rot, unless the manufacturer installed a non-marine carpet, which would be pretty lame. The carpet can wear out, stain, and rip, but it won't rot.

As for what's underneath, yes, the carpet will hold water and retard the drying out of whatever is underneath, so you should find out what's under there. If it's not gelcoated plywood, or at least pressure-treated plywood, you need to look very closely at certain areas -- transom corners, under the batteries, cutouts for hatches, anywhere that screws go into the floor, etc., and convince yourself that the flooring is sound.

Of the three boats I've owned, two had carpet and one had non-skid fiberglass. Ironically, the one all-fiberglass one was the only one that had flooring problems, rotting around one of the hatch cutouts.

Good luck, and regards.

Finegrain