On a boat, use a waterproof ammo box. When hunting by foot, toss your shells into a zip-sealed plastic bag to keep them dry from rain or if you wade too deeply when setting your dekes.
If you do get rust on the bases (which happens to all serious waterfowl hunters), dry them, then wrap a small piece of fine-grain sandpaper around the brass and twist the shell several times. Most of the rust will fall off. You won't need to discard the shell or worry that it'll jam when the ducks are pouring in.