Yes that’s correct. We should certainly look at adding a log for that - it can be very confusing if you are not aware of the feature. I will add it to my todo list.
If you’re running the latest version of Discourse, then we have recently added some extra checks before deactivating admin accounts:
https://github.com/discourse/discourse/commit/836b3f4d82dfc610574db93cfd1d86e4064d4062
If the user has created posts, or has a recently used API key attached to it, then it will not be deactivated. Note that the API key must be specifically attached to this user, and not an “all users” key.