For PDF Explorer, this would suggest an optional setting which allows the user to specifically give PDFE responsibility for creating and managing subdirectories for optimal disc performance.
This feature would appeal to users with very large collections, such as universities, insurance companies, engineering and aeronautical firms (NASA), and governments.
So your idea is to have some kind of automation to disperse all the files by no important name directories, automatically created when the one been used reach a defined maximum number of files by folder?
In a NTFS disk we can put 4 billion files in a directory. The problem of big number of files by directory only occur when browsing by directory, because all the file names, and associated metadata, must be read into memory to perform a simple tasks as sort by any of these metadata attributes.
When searching for a file, search operations, not browse, are used, and the possible big number of results is the problem, not the number of files by folder, so, in this case your idea works ok.
Tree categorization is also a good way to organize and search for. We can use your idea of non categorized one level directory structure and create later a virtual categorization tree, but, why not use the physical disk directory tree to get, at least, a simple organization from the start?
The "Extra>TaskAutomationFolders" functionality can be used to achieve any of these goals. With a new tool to execute your idea, and, if the renamer tool can also create folders using metadata for names, achieve the second, more usual, approach.
