How is in-game currency awarded – is it based on how well you complete a mission? Percent based on enemies killed? Etc.

The amount of cash stolen, and in the case of when you acquire goods (drugs, equipment, etc.) you can sell this off to make money too. 

Each mission has a goal – e.g. bringing 9 bags of loot (jewelry) and this goal is worth a certain money. Nasara plans the optimal amount of loot that he will be ready to convert to clean cash. The cash reward (how easily can Nasara transfer into clean cash) is then based on performance (achieving this goal, not harming any civilians, guards, not leaving anyone behind or fulfilling some special bonus objective). Greed is an important factor, so players can try to steal more than what is the goal. They put themselves in danger but they can keep extra loot. What you steal on top of that planned loot, will remain in the form of the loot, that is possible to sell via black market later.

Teammates will take some cut, so it’s not wise to send too many people on easy jobs etc. Earn more money by doing missions with Baker himself (as he is the boss and not taking the cut for himself).

There is no reward or bonus for killing enemies. But sometimes the goal is to eliminate a certain character or group of gangsters as part of the turf war effort.