In the long run, it does not matter -- either way is fine.
The USERID is stored down in the projects related to transactional, author/assigned-to type of information on various records, but QC really does not ''check'' to see if the user exists after being stored as part of a record -- it is just a string at that point.
So, for legacy information like ''who opened that defect'', or ''who changed the status to that'', the data is still there.
Now, if you want to find out about that user or send them email (from within QC), it cannot do that if the user is gone from the user list.
The users list in Site Admin (a ''global'' list) can get unwieldy as more users are added and various ''old'' users are disabled through attrition. It would make sense at some point to ''retire'' old, unused user accounts by deleting them from the Site Users list. You can always re-create another user (and add user to various security groups as before) with exactly the SAME UserID if that person joins the team again and it would pick up where it left off (on the record level).