And that is precisely why Military ships in Aurora have maintenance costs and commercials do not; You just explained it perfectly.
If something breaks on a Commercial ship, it is very unlikely to be of any critical importance, and can be fixed in the next port without much hassle.
If on a Military ship something breaks, it needs immediate fixing, which costs, while on the civilian freight transportation, is is cheaper, and thus can be abstracted away easily.
With the current systems, a Freighter would need roughly 5000 tons of pure engineering spaces and several hundred men maintenance crews, when that in fact does not happen.
On a big freighter, there is simply nothing important that can break, short of the engine, and why would you inform the player 20 times in every 5 day tick that something on one of his ships has just broken and was repaired by the sole engineer of the ship, requiring a tenth of a maintenance supply? That is work, and it's work that the player can delegate to the inner workings of code, because no one cares.