The thing about that that bothers me is if you look at it from the rules perspective, money for a completed run is meant to cover the cost of resupplying/healing/recovering, plus maybe some extra if you do well. Okay fine, great. However, from a flavour/roleplay perspective that's just dumb.
Any intelligent Mr Johnson knows that if the runners happen to pull off a job quickly and easily(I.E. easier than expected), and he tries to pay them LESS for their success, he either risks word getting out about his sketchiness and good luck finding runners next time, or he encourages runs to get more messy, so the team can get paid more. Either one is a bad option.
More likely he'd be encouraged to offer hazard pay if his intel was either inaccurate or didn't cover everything, or to pay based on the professionalism and efficiency of the team. So if a team was more skilled or performed at a higher level than anticipated, why wouldn't the Mr Johnson pay them an incentive to keep them operating on that same level? Likewise, if they completely fuck things up and cause royal drek to hit the fan, the team might very well get a reduced payout(say if Mr Johnson's backers now had to do damage control), or be lucky to find continued work from him/her at all.
Anyway, that's my two cents worth.