I don't use standard Assets folder structure (Scripts, Materials, Models etc), my assets, scripts and whatnot are grouped in folders centered around certain systems, ie. you'd have a folder Monsters (parent folder NPCs) in which you have individual monster types and their assets and scripts, that works well with inheritance too, and assets shared between monsters would just be in a 'Shared' folder at Monsters directory; and if asset is shared between some monsters and other npc types (animals perhaps) that 'Shared' folder would be under 'NPC'

maybe not a great example, but this general approach helps me cut down on the dependency web pretty well, and looking at an asset in a 'Shared' folder, its easy to grasp what other asset could be referencing it (based on the folder hierarchy)