johnny1 is right:
It is not so straight-forward how to hide a folder again, once it is unhidden.
There is already a small menu next to the folder's name. It includes unhide, but no Hide options. I suggest you could include the Hide option right there.
The benefit of a nice app like this is, among others, to very easily and quickly hide all the things we want. We usually want something to be "open" only for the time that we use it. Then we close it.
As johnny1 mentioned, it is not so easy to find how to hide a folder again. Closing the app is OK :-) but not quite logical that I have to shut down a complete program if I want the program to do something.
A better solution were, I think, to make it a bit easier and include a Hide (again) option somewhere for any enlisted folders. Maybe in the already existing drop-down.