I have an A.R.E. shell on my Tacoma, and yes, some water gets in around the tailgate in heavy rain. I have put foam all around, and there is less water. Also dust gets in, when I drive in deep sand. But I don't think the water or the sand have anything to do with the shell. The tailgate is just not even close to water-tight.
There are after-market gasket or weather strip kits that you can buy. I don't know how well they work. If we have "water sensitive" cargo (such as the generator), I just load it into the truck bed in a big plastic tub to protect it.
And I like this shell -- the hatch locks, and the side windows open, enabling me to reach cargo from the sides. And the windows lock, too.
