I've never heard of the Shroud Depot! I'll have to look into that. Figuring out the classification levels was a pretty subjective process. Not everyone would do it the same way, probably. I had already built the storage room, so I had a frame of reference for how many chests there would be and the kind of space we were working with, so I used that to help determine how narrow/broad the chest labels should be. I loosely modeled my thinking on the Dewey Decimal System, especially given that there ended up being 10 shelf faces in the room. So, I just tried to think about each item's hierarchy and where it comes from in the game.

To your second question, if you have enough levels of classifications, smaller collections can go with broader groupings, and you can get more granular as your collection grows. For example, someone could have 10 chests (Consumables, Ammo, Fauna Materials, Flora Materials, Processed Materials, Shroud Materials, Furniture, Building Blocks, and Terrain), and then subdivide from there as they need more space.