custom_hooks_dir setting in config.yml.example is no longer relevant
In https://gitlab.com/gitlab-org/gitlab-shell/-/blob/master/config.yml.example#L34-36
# Parent directory for global custom hook directories (pre-receive.d, update.d, post-receive.d)
# Default is hooks in the gitlab-shell directory.
# custom_hooks_dir: "/home/git/gitlab-shell/hooks"
is defined but is no longer relevant in gitlab-shell as it's now setup in gitaly.