So I've got some cargo ships pushing facilities to an asteroid rich in Corundium, which I need to produce more mines. Only issue is, my cargo ships are all "Whaa, we've been out in space too long" and morale and shit. I've got 3 ships and need to move like 100 automines. How do I fit it into their cycle orders to take shore leave?
I understand your problem. There is no "wait till shore leave completes" command, so you really just have to stop the cycle and hang out at some populated colony every once in a while.
Hence why my cargo ships typically have over a year's worth of crew quarters.
As for other solutions, I'd suggest issuing civilian ships contracts to ship the automines, then dump money into the shipping companies, preferably one that already has a cargo ship: it seems some companies won't do both cargo and passengers, and the names are downright misleading (cargo company only ferries colonists? settler company only does cargo? WTF???).
I'd also suggest redesigning your cargo ships to add more crew quarters. You should be able to retool them at the same shipyard the made them, if it's still tooled to make cargo ships.
I *think* cargo ship crews get shore leave when the ship is loading and unloading from a minimally-populated world. If so, it might be worthwhile to rip out those cargo handling modules that would ordinarily be highly useful (10 days of shore leave should covers most deployments).