If you scan a ground target, discover they have a bounty, and then kill them you won't get WANTED status. If anyone else sees you scan them (including the target), they will still go hostile. It can be an important distinction when dealing with non-anarchy bases. When dealing with anarchy - kill them first, scan later. Also, preferably shut down settlement alarms before going on the killing spree.
As far as cleaning out an anarchy settlement, or scanning scavs in a derelict settlement, you can earn betwen 100k and 300k of credits. No, it isn't a lot of cash, but it does add up. Also, turning in those bounties increases your reputation with the factions that issued them (I often have 5-7 different ones when turning them in later). Better rep means better mission rewards from those factions. Far from pointless.
Uh, no. Mercenary rank, just like Combat (ship) rank, is gained based on the targets rank in relation to yours. Exploration, Trade, and Exobiology are affected by how much money you turn in, but not the combat ranks.
The only way I'm making ANY progress (currently Gladiator, grinding towards Deadeye) on Mercenary rank is by doing High Intensity combat zones. Depending on how many I kill, I will earn between 9 and 17 million a run. The bar barely moves. I have to measure it by noting where the tip of the bar is lining up under the text above or below it and then comparing that after the battle is over. The progress is incredibly slow (the grind from Deadeye to Elite is going to be horrendous). Also, the progress happens as I make the kills, not once I turn in the combat bonds. I always check for the progress, and how much money I will have to turn in, on the flight back in the Frontline dropship.
As far as I know, the only way people are cheesing Mercenary rank is by going to the site on their own (not enlisting), and rapidly destroying everyone on both sides with the handheld missile launcher. I prefer to actually enlist, get the free transport, and gain rep with a particular side.