Typically I use one folder for all Static Meshes. For models that will be animated, I have the model and associated files bundled. Single directories for textures and such.
You seem to be missing the point though. The point is not whether or not my file structure is bad. My file structure works for me. Could it be better? Sure. The point is that, as I learn, I should be able to fix it as I go without having to worry that my entire project is going to get corrupted by the way the engine handles the linking/referencing. No amount of preplanning is going to change that simple fact.