In your original post you said that you were just using the filename to check existence. If it has data, then a file is more reasonable. However I would still suggest looking at something like DB_File's interface to Berkeley DB.

That's designed to store data of exactly this type. Its data limits are 4 GB per entry, and 256 terabytes for the entire dataset.

If you want to store the data on one system and use it on another, then you might want to move up to a database. Sure, there are things like NFS. But if someone goes innocently looking at a directory like that using standard tools over a networked filesystem and you'll be putting everything through an "interesting" stress test. Plus even though it works today on ext3, that's no guarantee that in 2 years someone won't migrate the system to another system and not understand that that directory really, really needs to be a specific filesystem.

While I agree that there are things that belong on filesystems, this feels to me like something that would be happier not living on a filesystem. But if you put it there, then I'm going to suggest that your disks will be happier if you turn off maintenance of last access time in that directory. That information is almost never used, and causes every read of a file to write to the directory. If you're under load this can be a significant cause of overhead.