When Deleting packages from SCCM Console it leaves the empty custom folder in the DP and only Delete the content of the folder.
Custom folder created during package creation should also get deleted from DP when the package is being deleted.
As of now whenever a package is deleted from console it deletes the content of the folder but leaves the empty folder itself.
These empty folder has to be manually identified and then cleared from the DPs.
This process of identifying and deleting empty folders is cumbersome specially when having large number of DPs and requires special attention while doing in order to avoid removing any of the working folders mistakenly.