Soft links (shortcuts)
Shortcuts can easily be created with the Windows Explorer. Just remember that they can only be used for scenery packages in the Custom Scenery folder.
To create a shortcut: go to the location where the actual scenery package is located (source), right click on it and select copy:

Now go the Custom Scenery folder of X-Plane,right click again and select ‘Paste as shortcut’

You will see the shortcut down below:

If you want you can remove the ‘ – Shortcut’ part in the name.
X-plane will ‘translate’ the shortcut for you. In the scenery_packs.ini file you will see this line:

Hardlinks (junctions and symbolic links)
To create junctions and symbolic links you will have to start the command prompt (for symbolic links you will need to select ‘Run as administrator’):

If you type ‘MKLINK’ you will see how to use the command:

To create a symbolic link (1st example) or junction (2nd example) you type:
MKLINK /D "D:\X-Plane 11\Custom Scenery\BIKF Keflavik" "E:\Airports Europe\BIKF Keflavik"
MKLINK /J "D:\X-Plane 11\Custom Scenery\BS2001 Object Library" "E:\Airports Europe\BS2001 Object Library"
And the result in the Custom Scenery folder (symbolic links have a green arrow and junctions have a gray chain in their icon):

For X-Plane these links are normal folders. Windows handles everything in the background and X-Plane does not need to know that they are actually links.
Deleting
Shortcuts, symbolic links and junctions can be deleted without problem: the original folder will not be deleted.