Outside mine like going under, inside they like going higher. Could be they can't trust their rooster and have to be brave themselves. You would know by a drop in egg production or if you see lots of shell less eggs that it's too much stress on them. Who knows maybe they enjoy being scared too...
I throw things all the time, my chickens get used to it, yours seem over reactive. I wonder if you are having other visitors to your coop at night which is making them more nervous. I see you have a rooster which should make them more secure feeling. I still would try to block some of their...