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One of the reasons could be that management programs expects that folder to exist. If the code is not robust, a missing folder with cause the program to fail.
Also, if the folder is a mount point, it will be outright wrong trying to delete it.
And it may be the administrator's human preference, to have certain folders or folder structures always in place under all circumstances.
Generally speaking, this feature seems to be an example of over-engineering. There is no good reason why Domino should delete empty folders either.
Can you please describe why you want to keep an empty folder around all the time?