I assume you're refering to FileDocument storage?
Uploaded files are put in subdirectories for performance reasons (1000 per folder). When huge amounts of uploaded files exist in the same directory, browsing, making backups etc. gets sloppy.
Example: for document with object store id 13456, the file document path will be "deployment/data/files/013/13456" (subdirectory names are prefixed with a zero as they otherwise conflict with "older" (pre 2.5.1) uploaded files when using mkdirs()).