ok, bear in mind this is complete supposition on my part, and isnt actually supported by any evidence.
I dont think that they would have actual 'trading ship' 3D units. They may have icons on the map, or they may just have the route. I think that you could then assign 'convoys' (either to the icon or route) to defend it. how this would be implemented, as you wouldnt have enough ships to defend all your fleets, i dont know. Then, if the enemy raids a convoy a battle would break out, but if it were undefended the attackers could probably just destroy/steal most of it.
Just my thoughts-remember, this could be (and in fact probably is ) totally wrong.