We have hanging pockets over the head of each bunk that holds things but it seems to me if you are putting in shelves they would work better at the foot end.
When we have smaller grandchildren we put a Rubbermaid container at the foot.
It serves as both storage and a desk while they are awake. Do not know if either of my idea would help you but suggest if you are putting in a shelf you look at the area at the foot and not at the head end. Our head faces the bunk room TV but that does not mean others have to.