I doubt many people in this forum run in places with more moisture than me; I live in Panama (the one in Central America, no to be confused with the one in FL), and wheel here and in Costa Rica. I have both carpet and hard top, and yes, it is the carpet that will hold the moisture. My hard top is in dire need of new weatherstripping, as when it rains, the water puddles in the passenger side floor and the rear of the Jeep gets nice and wet... Still, nothing like decent insulation to make the AC cool on 110* weather! I would not get rid of either. Actually, I replaced my carpet about a year or two ago with a mossback one, and could not be happier!
EDIT: I do take the carpet out of the Jeep when I go wheeling, but it is usually in there. If it gets wet, I will also take it out and hang it in my house so that it dries up.