Stating the obvious probably, but often even the obvious escapes me 
The cheapest way to extract minerals: manual mines. Then, Orbital Miners, but they are restricted to small bodies (can the body be populated? AM are fine though). And finally, the costliest option, Auto-mines.
I'm asking because I'm just starting with OM and it seems like a good middle ground. Although you need tugs to move them, and they can't be refitted unless you have a shipyard for them, which I don't.
Orbital Miners are the best way to mine.
You get the same productivity as a surface mine for the same cost, but it is 20% the size and does not require population to run.
The overhead cost to put the modules on an armorless space station is minimal.
The cost of a simple 5-module station is 86.7% modules. So the cost of overhead is about 15.3% of the cost of the modules.
The cost of a 50-module station is 88.6% modules. ~12.8% overhead.
The savings is in the cost of transportation.
To move a surface mine, you need 25kt of cargo hold, which runs empty in one direction.
To tug a 5-module orbital mining station, take the cargo hold off of your freighter, and replace the cargo shuttle bay with a tractor beam.
The outbound haul will be at roughly the same speed as before. The return trip will be faster. How much faster depends on the size of your tug relative to the station. Assuming roughly 1:1 size, the return leg is at 2x the speed of the outbound leg.
You now have a smaller and cheaper ship moving 5 times the mining capability in round trips that take ~25% less time, and which do not have to be accompanied by even more ships carrying population and infrastructure.
