So basically Far Cry 3 thing that everybody wanted but never got. (I just made a gamesave with the main game beat but no outposts so I could reload every time.) But there were tons of those in that game, I doubt there are that many in comparison in AC4, but I haven't played it yet. It's not a bad idea, adds replay value. I don't think it will see the light of day though.
So far, I'm up to Sequence 6 and I really love the Plantation/Warehouse concept but I really think these Warehouses should "refill" after a certain number of hours or in-game days. Who else would like this or think it will ruin the game? But if it were to replenish it should decrease the amount of reward you get from it since you last stole from it - and increase back to it's original reward after 'X' amount of times.