What makes you think the "Thumbs.db" file is the source of the problem ?

I'm asking because some RAR files are not correctly processed by the library Ubooquity uses to decompress them. Decompressing and recompressing them usually solves the problem. So the fact that your comics work after removing the "thumbs.db" file might just result from the recompression step, not the file removal.

I don't know the first thing about Bonjour, but I'll take a look.
Can't promise anything yet though.

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.