I always carry canoes upside down, they tie down better and don't
accumulate
rain water. Kayaks, I always carry right side up since their bottoms are
flatter than their tops and therefore easier to tie down (and their
cockpits
are small enough to not accumulate large amounts of rain water.
Rick

The only reason I carry my sea kayak with the deck up is because the Yakima
cradles I have are set up that way. I'd carry my boat hull up if I could.
But you can always put on a cockpit cover. I don't know if they make them
for sea kayaks, but for whitewater boats you can buy a gear bag that doubles
as a cockpit cover...