If I change core.hooksPath to a folder (.githooks) different that .git/hooks/, and the post-checkout hook writes a file in .git, git subrepo pull fails as follows:
$ git subrepo pull aux
git-subrepo: Command failed: 'git worktree add .git/tmp/subrepo/aux subrepo/aux'.
Preparing .git/tmp/subrepo/aux (identifier aux)
HEAD is now at fcf0b6a verification of mechanical requirements
/path/to/project/.githooks/post-checkout: 15: /path/to/project/.githooks/post-checkout: cannot create .git/gitHeadInfo.gin: Directory nonexistent
This happens also with the default core.hooksPath setting