I have personally never seen the 0-byte files people keep talking about here. In every S3 bucket I’ve ever looked at, the “directories” don’t exist at all. If you have a dir/file1.txt and dir/file2.txt, there is NO such object as dir. Not even a placeholder.
So essentially an S3 file manager must be able to handle the situation where there are files without a "directory"—and that I assume is also the most common case as well for S3. Might just not have the "directories" in the first place.