Ubooquity already has an option to hide empty folders. Check the "advanced" settings section.

It was part of the initial design I had in mind for Ubooquity. So I might add it in the future.

It's a bug introduced in 1.7.0.
It will be fixed in the next release.

This warning ("Could not understand cookie header") is triggered by the cookies created by the Synology interface in your browser. It can be safely ignored (and I should probably remove it).