cosmetics, just prefernce mostly, also i think the cover impedes the p/us, like blocks them slightly, not noticable of course but some people are picky
Mostly just for looks. Some say it'll affect your tone, but it will be HARDLY noticable.
apparently UG's only type O-

Quote by Strike9

Thanks jb_designs.
Quote by xxgenocide98xx
It slightly reduces the treble.

Exactly. Covered pickups are a bit less bright sounding, so you might want to hear the difference before buying. Chances are you won't really care too much, but it's worth testing.
If you have cover-less pickups you can get some sheet metal and cut out dimensions of your pickups then weld it so you have a cover, the magnetic field the pickup produces should hold them for you unless your using something super heavy. The difference isn't very big, I can't even tell the difference when im playing with other people.