If a repo is cloned using git clone --single-branch --depth 1, git-annex-init and git-annex-sync do not seem to correctly fetch the git-annex and synced/git-annex branches. git-annex-info does not list remotes that were known at the cloned repo.

This is not a bug. You have cloned a repository without cloning the git-annex branch, so as far as git-annex can possibly know, this is a git repository in which git-annex has never been used before.

As soon as you fetch the git-annex branch from origin, git-annex will know all the information that you expected it to know. So all you have to do is: git fetch origin git-annex

There is no possible change I can make that will prevent or amelorate this particular means of shooting yourself in the foot.

done --Joey