Somewhere in my museum research it seems to me that I read that the height of the stacks was at least in part determined to be as tall as possible and go under bridges. This was because one of the greatest enemies of the steamboats was fire as they were made of wood. Therefore the taller the stack the less chance of hot embers and/or sparks from the burning wood would have to land on the boat and start a fire. This is said to be one of the reason for the crown or feathering on top of the stacks. I admit this isn't very scientifid, but makes for a reasonable story.