Does the scoop opening have any kind of mesh in it? If so, snow shouldn't be that huge of an issue. Unless it's a super-fine snow that won't stick for crap, it ought to pile up over the mesh about like it does on the rest of the car. When you brush it off the car, some might fall into the engine bay, but I can't imagine it would be enough to cause problems.
As far as water goes, I wouldn't worry too much, unless it's running right down onto an open air filter.
I'm sure a simple piece of cardboard over the opening at night would work as well as a cover, though some might consider that "ghetto engineering."
My two cents, and that's probably over charging!
