We use it to store petabytes of large video files and our system is structured such that no folder ever has more than a couple files in it (>20 is rare). With properly tuned caching this works fantastically well for our use case and I would take the simpler code and reduced points of failure over NFS nonsense any day.
That of course doesn't mean s3fs is the solution to every problem, it simply means it's good to have options and don't write something off because it "might be slow."
Know your data, know your use case, and know your tools. You can make smart decisions on your own rather than driven by anecdotal comments on HN.