And his second, and third-hand man. I world traveled to the fort, and killed them.

Does this affect the story line? What happens when I finish for the NCR, and there's no Lucius to fight? Or does it spawn a new lucius?

Do you mean http://fallout.wikia.com/wiki/Lanius

If so, you still fight him if you side with the NCR, and killing Ceaser does affect the story, but not in a bad way if thats what you are implying.

Legate Lanius is Caesar's second in command. He's not at the Fort so you can't kill him. You'll still fight him at the end of the Battle of Hoover Dam.

You can get a better outcome with Chief Hanlon now if you're on the NCR path.

Cool.

You did the game world a favour and got rid of a scumbag. Much better storywise I think. I always kill Caesar.
Also people mention it. You still fight Legnate Lanius at the end.