I have one of the plastic boxes. Although I have not used it for years, it did get regular workouts when all the kids lived at home. The one I have uses nylon straps and hooks to secure it to the roof rack track so it is fairly easy to install and remove at will. I have seen others that secure to the racks themselves with u-bolts right through the bottom of the cargo box. They are more secure, but need some time and a stepladder to install/remove. Mine hinges on one side with locks on the other so it is pretty easy to load and unload too.
It's not particularly aerodynamic, but I never noticed (or at least, don't remember) any noise from it. Of course, whenever it was in use, I had a car full of kids...
Thule makes a couple of nice aerodynamic looking models that feature a quick-release u-bolt system they call "Easy snap". They claim it will fit most factory roof racks. I have no personal experience with them, but would certainly be looking close if I was in the market today.
My brother had one that hinged at the rear and was a PITA to load/unload, especially on his taller mini-van. It did not have a lock, just a latch. The latch popped open one day, the wind ripped off the cover and they all had a 3 hour ride home with their recovered belongings piled on their laps.
I would not rely on any of them to be completely waterproof. A heavy downpour at highway speeds will almost certainly allow some water entry somewhere. Canoe pack liners will protect your stuff though.
Another consideration: storage when not in use. I have mine stuffed up in the rafters of an out-building, but some people may not have enough room to store the thing. At least bags collapse when not in use.