Close them, always.....
I always close my thru-hull valves when sailing, and when I leave the boat alone. You can open them if you have to use the head or galley sink while sailing. Sailing with the valves open invites water into the boat via the syphoning effect when the boat is heeled. Installing vented loops will lessen the chance of syphoning. See the Headmistress Archives for in depth discussions of where to place the loops.
