I also experience storm effects in a second layer cave but not always, sometimes there is a storm and it doesn´t "go" into the cave but sometimes it does and then I get the dust and the swaying tethers but I haven´t seen rocks go flying or been killed by this. I think maybe somewhere I haven´t discovered yet there is a direct opening the storm can get through so it only happens if the wind direction is a specific direction. I don´t know if this is supposed to be this way, if it´s a bug or if it is something else