When I experienced the same problem but on a smaller scale, I resolved then and there that all of my hooks would be stored in their original containers with the original facts about each hook model number, type, size and manufacturer. I use a small chest of drawers such as is available for screws, nuts and bolts at the hardware store to store all hooks in their original packages or box. Each drawer is labeled accordingly.
Also, I sort my hook types by dries, wets & streamers, nymph, midges, saltwater , bass and blugill. This probably sounds anal as hell but it is working for me. I also make use of the little magnets that come in the Tiemco packages and also cut sheets of magnetized material for each drawer bottom.
When working at my tying desk, I remove only the amount that I will be using at the time and they are placed on a magnet that is on the pedestal base of my vise. Love those magnets!!!
Finally, I have a small spiral notebook where I maintain a record of the inventory and thus know when I need to replace used up items.