Mine is fitted with a hard top, but I often hose out the back.
Any water that is left in there runs out through the gap at the bottom of the tailgate when you start moving.
I cant see you getting rust problems unles the paintwork is scratched down to metal. Unlikely if you have a load liner.
One thing to note though, mine is fitted with a removable load liner and this leaves nowhere to tie things down.
Cheers
Steve