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Since the hull is fiberglass the wood exposed to ballast water is the fore and aft ballast tank bulkheads and the bottom of the sole. If these are properly coated with epoxy resin and fiberglass or another waterproof coating, such as Sani-Tred, the should be no "rot" problem.
If your boat is in salt water, the primary problem with leaving the ballast water in the tank is all the stuff that will grow in the tank. Adding clorox to the water is one way to solve this problem. I choose to go the bilge pump route as shown at http://penncove.tripod.com/Skylark_Fill_Drain
The concern about leaving an unballasted boat on a mooring is reasonable if the mooring is exposed to extreme winds and seas. See my post here on how I addressed this issue. http://bbs.trailersailor.com/forums/santana/index.cgi/noframes/read/4208
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