They are not meant to be waterproof. How else would your window slide up and down otherwise?! Hence, as said, there is the plastic sheeting to prevent damp getting to the vital areas (speakers, inner door membrane, etc).
Also you have drain holes at the bottom of the door. They are there for a reason. If you try to seal the black sections you'll just look like a muppet when you try to wind down the windows.
And silver_si, you're most definately correct 
Edit: My £200 DLS's have be fine for well over a year now.
