I prefer a flat file structure. I have one level of folders, with each folder corresponding directly to the name of the asset type (Blueprints, StaticMeshes, Textures, etc) and that’s it. No sub-folders beyond that. I don’t bother thinking about how to organize and nest folders into hierarchies like Content/Environment/Buildings or Content/Player/Gun.
I also don’t prefix my assets with BP_ or SM_. If you change the Content Browser view option to list mode, you can clearly see Blueprint or Static Mesh written below the name. Instead, I have a clear name like PlayerHmd (head-mounted display). The blueprint is called PlayerHmd, the static mesh is called PlayerHmd, the material is called PlayerHmd. Although the PlayerHmd assets are distributed across different folders, finding all the PlayerHmd assets is simple using the Content Browser filter (or the super handy Ctrl+P for quick open).
A flat file structure works if you keep a consistent name across asset types and leverage the search/filter tools. It also avoids duplicate assets.
Why flat? I’ve seen as many as 4 people stand around for over an hour debating where assets should go in the hierarchy – it’s crazy. Eventually, they all come to a fragile consensus (from exhaustion talking about it). A week later someone commits assets that don’t conform to the hierarchy and the debate continues…