Coming from a D&D standpoint, overcoming encounters/obstacles with no combat and actually using skills/wits/intelligence is far more worth rewarding than danger pay. Yes, things can get dangerous with lead and mana being thrown around and those should be considered at the end of a run when pay has to finally be dolled out. A good negotiation scene with a Johnson should reflect that, but shouldn't be the dominant factor. I think a Johnson can be rather indifferent about pay being dolled out because one of the runners got knocked out and was close to death. It's part of the danger of being a Shadowrunner in the first place.
It is good to plan out your payments a little in advance and leave yourself wiggle room to be open to increase/decrease payment.