Indeed, a folder is not empty if it contains a folder (no matter whether the inner folder is empty).
Theoretically, one could list those "recursively empty" folders but in practice there are several problems with that: One would have to couple implicitly selections of folders to be deleted (which might be confusing), the order in which folders are deleted becomes less transparent, and last but not least, some people would like to keep the "outer" structure of folders.
Instead of presenting a more complicated/confusing user interface, it was therefore a design decision to just possibly require several "clean empty folder" steps: The maximal number of repetitions necessary is the length of the deepest path consisting only of empty folders. In practice this should be far less than 10.

Thanks for the suggestion.
Version 5.9 provides now a button which moves the marked bookmarks/folders to a “Dupes” folder (instead of removing them).