As a former HK I did not see it as a cost issue rather a guest service issue. If the guest has a confirmed reservation for a bottom bunk in a 4xbed dorm is the hostel obligated to provide one? I always try to look at any issue as if was me that it happened to. If there was no resevations for that dorm room than first come first serve. What if the hostel is marketing itself to older travelers that may have a hard time climbing up/down from top bunks? I agree it can be a very hard system to maintain, but is worth the effort for the sake of the guest that reserves the bottom bunk.