This is because there are hidden LaunchDaemons and LaunchAgents keeping them around, which aren't accessible through the typical macOS interface. Unfortunately, with these types of unexpected events, removing the app from login items isn't enough to solve the problem. And unknown processes can drag on system resources in the background. Safari might redirect to adware sites or change its homepage without your permission.
An app might appear in your menu bar but not in your login items. Hidden login items can cause all kinds of problems for Mac users.
