I know how this happened. See in Season 2 episode 6 the Blackhawk Satellite lazer thingy was going to destroy the base, but Superman pointed the lazer ray out into space. I think the ray he pointed into outerspace destroyed everything in it's path, thus you have a huge blank section of space.

Jayne Cobb: Shepherd Book once said to me, "If you can't do something smart, do something RIGHT!