Ahh I didn't get that from your initial post.
What if you used PHP to decide what folder to put them in. For example, lets say you wanted to have only 1000 users using a particular folder.
Assuming their UserID is set to auto_increment,
ceil(userID/1000)
examples:
UID = 400 -> 1
uID = 1100 -> 2
uID = 4250 -> 5
This is a rough estimate as you will realistically have gaps in your userID, but it's a way to ensure you never have more than 1000 users sharing a particular folder.