Some weapons break a nest open when they hit it. Others just knock it fall down. If the nest has an item in it, it will release that item right away if it's broken open or release it after it hits the ground if it's just knocked down. The hookshot, bombchus, and zora fins break nests opens. Arrows and deku bubbles just knock them down. The nest in the hookshot room will only release bees and trigger a cutcene of scaring the pirates away if it's knocked down and not if it's broken open.