We don't actually know that it will be a problem. If the game is 1000x faster, you'd need to play the same empire for years to get that big.
If it does turn out to be a problem, the only real solution is to not track civilians 100% of the time. You instead would abstract them away. Instead of tracking each individual ship, you track the trade-routes they're on. The amount of trade that gets done is easy to calculate, it's just the average speed of the ships on that route times the average cargo capacity of those ships times the average speed, divided by the distance of the route. When a hostile ship gets close to sensor range of the route, do a dice-roll to see if any ships are nearby. If yes, you pull one out of the abstraction and spawn it on the route. If the hostile gets destroyed or the civilian gets far enough away, de-spawn it and put it back into the abstraction.