I've played 2-player Waterframe all of once so this is conjecture but I'm guessing it is for balance between shipping and the local markets. I jumped on shipping early and managed to snap up all 30 shares whilst still being able to upgrade my factories in a timely fashion. But to do so required plenty of planning (and, ideally, an opponent who starts shipping a lot later). I still only won by one share's value.
Perhaps the larger ships are simply too powerful in a 2-player game.