I expect others will have a different perspective on this, but our experience is with Active Directory (AD), and Tableau Server has a built-in feature to do scheduled synchronization of AD groups. While the synchronization adds users and removes users from the AD groups on the server, it does not remove the user entirely from the server. (I don't think you'd want it to, since the user might still be in another AD group). Thus, the server administrator must identify and remove these users. If the Ninja tools could handle that, they would be somewhat useful, although you can create your own tools using the servers PostGreSQL data and tabcmd. Since our project structure has no resemblance to our structure, we don't use the AD groups for security, but create special groups to manage permissions at the project level. This is pretty easy to manage for us using the User/Group actions on the server, but then we don't have many thousands of users or hundreds of groups, so this might be more efficiently managed with an external tool of some sort. So, from our perspective, the Ninja tools are unnecessary.
If, however, you are using local authentication on the server, I could see where the Ninja tools (or other similar tools) might be very useful to keep users and groups up-to-date.