Covering, with shrink wrap usually, keeps snow from filling the cockpit and potentially plugging the scuppers so it floods when it gets a rain thaw. Also snow sitting on the decks will slowly melt and potentially run down around the stanchions into cracks in the gel coat and freeze, crack and repeat until it gets into the core.
But I just shrinkwrapped the back half of my Pilot 34. Avoids the stuff on the roof, but the shrink wrappers can handle that if you want to do the whole thing.
David
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