S3FS uses special 'hidden' zero byte files to represent directories, because S3 doesn't really support directories. If you try a mkdir on your mounted s3fs bucket then use the AWS file browser you should see this in action. If your S3 bucket contains a directory structure that was not created by S3FS then S3FS won't recognise that structure. S3FS only works well with buckets that are only ever manipulated using S3FS.
After trying to use s3fs for a project I was working on I concluded that it was better to be exposed directly to the limitaions of S3, rather than using something which attempts to hide those limitations.