The economic effects of navies is something EU2 lacks, severely. Thus, e.g., captures of treasure ships are reflected only by event.
An extreme example is in the Napoleon's Ambition scenario. At the start, there is a big French fleet in the Atlantic, heading home, with about 40 empty transports. This clearly is replicating the vital convoy, around which the 1st of June campaign was fought. This campaign ended in a severe tactical defeat, but a strategic success for the French; they got kicked in the battle, but the convoy got through. But of course, it doesn't really mean anything in the game; all the RN can possibly do is what they did, pound a bunch of French ships. There is no stategic/economic consequence beyond that.