As the title suggests, stopping the assistant through the terminal doesn't work as expected and I had to kill the assitant by hand, which in turn means, that git annex has to repair the repo. A workaround seems to be to start the assistant through "git annex webapp" and use the shutdown daemon button in the webapp. Before this workaround does work, you have to "git annex assistant --autostop" and restart, so that launchctl won't keep the daemon running.