what is the best way to organize the folders and the files for a solidworks project ?

I do not like this method for assemblies of less than 500 pieces. First, each file has an extension that makes sorting easier. Secondly, the name of the folder is not parametric. Third, Solidworks has steadily created thumbnails of parts, assemblies, drawings that facilitate selection in the window expander. Fourth is longer for backups and search. So the best method is to use the window explorer. Remember that Solidworks is native Window platform.

There is nothing wrong with that method.
When you say "big assemblies", how big are you talking about? How many unique parts are used? How many parts in total?

Each operating system and hard drive formatting option has a limit to the number of files stored in a folder. I think you'd have to try really hard to exceed 60,000 or 4,000,000 files in a single folder.

The biggest limitation of your proposed system seems to be that you'll have 90% of the files under Parts. Another 8% under Drawings, the Assembly and Sub-Assembly folders are going to be nearly empty (unless you have dozens, or hundreds of sub assemblies in the project).