Do the metal pickup covers make any difference in the sound or are they just for the looks?
Sometimes, they can be just for the looks. But, for the most part, they make a difference.
What difference do they make?
They add to the tone. It depends on what kind of covers you're talking about.
Remember that pickups are magnets, the covers will pretty much always make a difference. But they look so damn cool I think it's a good trade off :P
most people will tell you that the cover doesnt make a difference, its more for looks. and even if they do make a difference in sound, its almost unrecognizeable.