By using green labels in OS X BoxCryptor basically disables / overrides that function for any of the encrypted folders you are working with.
I don't think this is particularly useful feature because many people use the in-built colour labeling to order their files.
Additionally - I think it looks a bit ugly and I would prefer my directories to look as they do normally rather than a wall of green.
The solution I think is very simple.
Take a look at the Google Drive OS X application and you will note that upon successful syncing of a file or folder a discreet little "tick" is placed alongside the icon.
Simple, effective and should be pretty easy to implement?
I'd hope BoxCryptor can provide something similar.
Footnote: another user has put out a similar request in the past which seems to have been overlooked: https://forums.boxcryptor.com/topic/avoid-automatic-green-label-dot-in-os-x#post-6871