I'm not sure I understand your answer.
My civilian geo survey ship, with 3 months deployment, runs just fine out in the field for years, just like my civilian freighters, terraformers or sorium harvesters. On such ships I never change the default deployment time from 3 months, nor do I add any additional engineering spaces. I just add the engine, the fuel, and the working modules (cargo bays, terraformers, harvesters, &c) and then I lock the design and never think about it again.
That exact same ship, with a civilian jump drive bolted onto it, suddenly starts suffering maintenance and morale problems.
Any idea why?