I think if you made each system stand-alone, with limited contact between each other, you could get away with computing a lot of stuff when you dock or hyperspace?
You'd only be able to access last known prices in other systems from space, though the latest prices would be available in the station. So a lot of workload could be shifted away from Real-time? The only thing that could complicate matters there is ships jumping in/out of system?
Edit : Oh, and the 'X2 problem' I keep referring to is exactly the computational-volume problem you are concerned about, the game tries to keep so many balls in the air at one time (something like 100 systems with 30-50 objects in each system, including traders, pirates, bases and aliens), that much of the game is over-optimised, and still is alas jerky, especially when your own fleet increases in size.
2nd Edit : Also, as far as freindlies/hostiles are concerned, just have a Star Trek system that auto powers up shields etc if a ship locks weapons onto you?