Asharak, eliminating duplicate routes is not mutually exclusive with strategic decisions. You can still decide to trade totally the Empire A becuase they are farthest from you, but use several systems instead of just one. The strategic benefits and disadvantages still apply.
That being said, I think having many trade routes between two systems makes sense. A trade vessel cannot meet the demands (presumably), and with multiple you get more of continual supply of goods.
What I think is dumb and a severe flaw is that you can build umpteen (i.e., a lot) of starbases in a single sector fully loaded with trade modules and get the same benefit across the board!
What's strategic about that? All of your fleets leave from that system and you make a ton of cash.
There should be a serious diminishing returns for the same reason I think multiple trade routes make sense--a trade vessel cannot carry enough goods that can be spread to all of those starbases.
The more strategic scenario is to have starbases along the route in different sectors. Now you have to worry about protecting those bases "out there" which is much more difficult and requires finesss.
The way, IMO, that the bonus should be calculated
across modules across starbases per sector. The bonus to that module is dependent on the number of starbases with that module. The bonus from extra modules is exponentially decayed (say 50%). In other words, the bonus from a module in a system would be:
SUM (1..m) { (1-r)^m }, where 'm' is the number of modules. Using r=.5 (50%), the theoretical maximum you can get is 200% of the modules bonus (i.e, +10% becomes +20%). At three starbases with the same module, for example, the bonus is 175% (+10% becomes +17.5%).
I'm sure there is an approximation so you don't have to sum, but I can't think of it.
/ds