Hi Erik,
If you want to know where exactly these folders are being used you may go to Site>Utilities>File Server Administration, there you will get to know what all master folder are enabled, Anyways these empty folders are not going to occupy much of the space in your hard drive.
The reason why they were created is because you configured the vaults to createw folders automatically, As soon as one folder reaches its maximum limit it will become read only and the next folder will start keeping the data.
Hope this will help.
Thanks