I believe flaming shots will be turned to a single shot ability with cool down. This is for archer units and mobile trebuchets/catapults. The balance and ranges will all be tweaked and tested before release. Arrows will be less effective against siege engines, unless using flaming shot. while wall catapults will be necessary to bring down attacking siege weapons.
Well, what about Isengard?? They can't build wall Ballistas, are they just out of luck?