When I had asked for help previously, I had been using tile entities, but the community reacted like I had personally kicked their childhood puppy, so I switched to using WorldSavedData. The reason I use nested maps is to help with networking, since it was the first way I thought of to reduce the size of the update packets, but I will take a look into merging them into a single map.
As far as storing integers, I thought that it would reduce the RAM required, since this is being designed for a relatively large modpack, as well as that you can use CraftTweaker to add extra materials later on if needed.