It also seems that some “do one thing well” tools want to implement their logic using files. For example: each entry in a password database is a file (pass(1)).

Whatever overhead of such small files might not matter though if the problem space is kept “human sized” (whatever one human can be bothered to manage).

I used to have tens of thousands of file in git annex. I had to tarball (chunk) some of the things that I never really use in order to speed up `git annex fsck`.