Sebastian I digged a little bit deeper in the Nautilus Favorites doubling issue.
Some of my files I keep in an encfs encrypted directory. I realized that after mounting this encfs encrypted directory, an aditional file showed up in the favourites directory. In other words: I have a file marked as favourite in my encfs encrypted directory. This file only shows up in favourites directory, when the encyrpted directory is mounted. Thats the way it should be, I guess. But i got curious. So I opened another instance of nautilus and navigated to the favourites directory: now this "nameless textfile" I described in the previous post only appeared once.
Theses "nameless textfiles" are files, that are marked as favourite, but which are not availabe to the system.
I checked this by marking another file in the encfs encrypted directory as favourite and unmounting the directory.
After starting several nautilus instances and navigate all of them to the favourite directory, the "nameless textfile" now got shown 3 times, symbolizing the 3 as fvourite marked files which were not available.
Further I noticed that after unmounting the encfs encrypted directory, its as favourite marked files "stayed" in the favourite directory, without being able to open them, off course. Even after hitting F5 for refresh or closing and restarting nautilus, these files were still shown in the favourites directory. After killing nautillus, they were out of the favourites directory.