That depends on how you access them. If you only ever iterate over all files readdir(3) in a tight loop is as fast as it can get; but if you need lots of access

That depends on how you access them. If you only ever iterate over all files readdir(3) in a tight loop is as fast as it can get; but if you need lots of access to specific files, you will waste a lot of time reading directory entries just to discard them... If there is even a remote chance you will use standard Unix tools on your files as well, I'd go for the subdirectories.