Civilian and Commercial ships are two different things. Commercial is for ships without maintaince failure rates, Civilian is ships built and controled by your shipping lines and not you. Tho I get the terms mixed up myself at times.
I tend to handwave it as military ships being built to a higher standard, Commercial ships being more robust and lower maintaince. Commercial ships in government service are more merchant marine than unarmed navy ships, they're built to a different standard.
Although in meta terms I see it as limiting micro managment to where it's most meaningful; the decision to pull a warship off the front line for an overhaul or patch it with maintaince supplied and hope it doesn't explode adds more than 'better pull freighter #23346 of the infrastructure run', in addition to commercial ships being in use far more than military. It can be exploited, but so can SM mode.
As for crew, IIRC that only affects combat reaction speeds. A grumpy crew can still perform their duties, they just lose their edge and such, which doesn't matter overmuch unless you need things done quickly.
