If you have 10000 files in a directory, you may also be running into problems with the OS being able to handle directories that large. See my writup on this on a different thread.

Depending on the OS, you are better off (from a memory / OS standpoint) making your directory structure deeper, so that when the OS is opening the file, it does not need to read more than necessary. The wider / flatter the directory structure, the more resources may be necessary to get to an individual file (on open() for example).

--MidLifeXis