That depends, are you talking about the Shadowrun Adventures (like Splintered State) or the Organized Play Missions (like SRM05-01 Chasin' the Wind)?
"Mission" or organized play games are usually written as a per runner to allow for varied table size. Different times the mission is run doesn't change the payout simply because more or less players showed up.
Adventures are more likely to use a lump sum method. It is more realistic overall. After all, if someone has a job they want done, and they have an idea of how much they want to spend on it, why would that amount change purely based on the size of the team? Some adventures might still give a payout per runner, but that is usually for jobs where having more team members is directly helpful to a job, like mercenary protection-style or a Johnson setting up a personal army. Jobs where you are hiring runners with a "salary" and not just paying a team for a certain result.
