What if Civilian ships were abstracted away unless there was a hostile contact? The ships could exist as a series of steps, each step having containing a start point and time, destination point and time, and cargo. Each sub-pulse, the game would only have to evaluate the ships that have a destination time in the past (or every near future?)
So you a freighter might have
From Earth (2052/02/01 15:00:20) | To Mars (2052/03/15 08:30:20) | With 2 mass drivers
Then, those 2 mass drivers are deducted from Earth's inventory and the freighter doesn't need to have any processing time until 2052/03/15.
If a hostile contact arises, some simple linear interpolation can be used to determine where to instantiate the ships. So if it's 2052/03/01, that's (roughly speaking) 2/3 of the required travel time, so just pick a point 66% of the way between the start and destination and add the ship there. Any discrepancy based on orbital mechanics or whatever can be chalked up to the the less precise nature of civilian captains. Once the hostile threat is gone, the ship can disappear back into abstract land with a new start point of its current location.
With a system like this, there's much less overhead for ships in transit, just some date checks. Naturally things would slow down when the ships became real again, but we're used to that.