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.
LOL!
"My wife's love is what unites Krypton and Earth in my heart. Without it, without her, I truly would be in hell."