Crews seem to work a lot better when their paths are restricted despite congestion. A single missile launcher with a factory directly besides it is the most efficient, but when you add another factory on the other side, the fire rate actually drops as crew would walk through the launcher to the other factory every now and then, causing more congestion and having more travel time. The most efficient system is a single missile launcher with a factory besides it, it will drain the factory dry and your fire rate = the factory's production rate.
Next, having a large area for the crew to avoid congestion is bad for missile module designs as it just increases their walking time and they really like to criss cross from one factory to another. Compare:
The second one with the middle corridor removed is occasionally able to empty both factories at the same time while the other has crew bouncing between both factories, thus being a bit less efficient. A tiny bit of difference, but still significant and noticeable.
Also adding in extra doors between the missile factories lowers the efficiency of the crew as for some reason they would go down the middle, walking further, before going into the factory to get ammo.
Adding in a conveyor system makes the mess worse as crew seems more likely to take ammo and feed it to the launcher on the other side.This results in a lot of crew bouncing about and sometimes would drain one factory dry while the other is at max, meaning that sometimes your fire rate from 2 launchers/factories would drop down to 1 factory's production rate.
One last note: Set your modules to have the exact amount of crew required (maybe +1 to 2) as excess crew seems to be occasionally slowing down the fire rate as well.
I think the crew AI needs a lot more work as it is. Being able to set preferred supply routes manually and locking crew to supply chains would go a long way to making ships more efficient.
