Unlike images, binary files are stored in a subfolder per content type independently of their location in the content tree. With many files, the 32000 files limit that exists on most common filesystems can easily be reached, preventing upload of new files.

This can be fixed by splitting binary files in subdirectories, depending on their hashes, like it is done for ViewCache:

var/plain_site/storage/original/application/ff12e1b4895bb2a92e3290e17316fe63.rar
=>
var/plain_site/storage/original/application/f/f/1/ff12e1b4895bb2a92e3290e17316fe63.rar