Play Services, Play Store and Services Framework will update automatically regardless of your settings. Others such as Maps should just update through the Play Store and respect your Play Store preferences. So if they have as well that is odd.
Updates which are not part of a system update go to /data/app, so do use extra space. If that's 5% of total storage that's a bit big, if 5% of what was free we'd need to know what that was in order to comment.