Well the scratching is more noticeable on the black ones, definitely. That's because scratches in transparent plastic take on a whiteish tone, and the contrast with the black makes them stand out.
Scratch removers basically work by melting the plastic on the surface and smoothing the rough, jagged scratch surface so that it becomes more of a shallow area than a scratch, which because the depth of the scratch is so small, it'll just look new again. Don't worry about the "melting"--it's only a very small layer that is affected. If you can't feel the nick in the surface caused by the scratch, you've got a good chance of getting it out.
Other scratch removers actually add a layer of polish, covering the scratches so they're no longer on the surface, which changes the way light is reflected and reducing their appearance. These are often less effective.
That's a gross oversimplification and isn't entirely accurate, but that's the gist of many of those products.