Comment 1 for bug 1258336

IMHO it is a lot saver to remove the mount-directories, so you don't accidentally write unencrypted files. Also it would clutter the base folder extremely. I don't know how many stashes you use, but if you encrypt all your devices you have easily 30+ and it just doesn't make sense to have all those skeletons lying around.
Also, what do you mean by access the stash from a script? If you want to mount it via a script, you can use
$ gnome-encfs-manager mount "mount_dir"
and it will automatically create the mount_point when mounting exactly as it would when triggered through the GUI.

This is a design-decision and won't be changed as it is what 99% (or something like that) of the people want and expect. (Mount-directory exists: mounted, otherwise: not mounted)