On the credits and slaves question, it says that after the vasari became bogged down against the TEC, they assumed many of the trappings of their civilization. Remember that the planets you control are nominally human populated, so keeping the planetside economy similar to the tec one makes sense, especially given their managerial practice of just letting the planets be as long as they pay their taxes. I see slave labor researches as getting the infrastrucure set up for such a relatively desperate move, and the savings from enslaving everybody are represented by the boosts to your economy. So no, it makes perfect sense in the lore. They're merely using a more aggressive theme on their method of 'coercing' a planet to give them the resources they need. Makes perfect sense in the lore to me. Plus, space is a much simpler environment for the nanites to work in, making mining nanites'd be pretty expensive and also require more vasari to oversee, which are a precious resource to them, without giving the added efficiency of switching to forced labor. I think that explains both apparent disconnects.
Also, who said they aren't using nanites to control the slaves because it's easier than making nanites. They don't have to fight gravity with a proportionally huge payload or seek out the good stuff in a very data-rich environment, and remember that making stuff out of atoms makes it hard to incorporate complexity, which is notably lacking from their nanites (except the carrier's passive ability, but that's just too awesome to pass up making) Other than that, they all have a very simple task, and if they're executed right, you can make the stuff relatively.
For example, the ability that damages an enemy ship over time and sends the health back can be accomplished by creating a molecule that can bond with armor and reverses magnetic polarity when it does so. Hit them with a beam of magnetism that shoots them at the ship, they eat hull, and get beamed back by the same beam that hit them, and are then used to repair the ship. Not that hard. Mining, on the other hand is a nightmare if you actually want to make it efficient.