Why we wind up deleting user accounts
I'm surprised that you actually remove users instead of just disabling them. Care to expand on that?
At one level, the answer is that we remove users when account sponsors tell us to. How our account management works is that (almost) every user account is sponsored by some professor; if the account's sponsor removes that sponsorship, we delete the account (unless the person can find another sponsor). Professors sponsor their graduate students, of course, but they also sponsor all sorts of other people; postdocs, undergraduate students who are working on projects, visitors, and so on. There's no requirement to withdraw sponsorship of old accounts and it's customary to not do so, but people can do so and sometimes do.
(For instance, we have no policy that graduated grad students lose their accounts or have them disabled. Generally they don't and many of them live on for substantial amounts of time.)
But that's not the real answer, because I've glossed over what prompts sponsors to take action. Very few professors bother to regularly go over the accounts they're sponsoring and decide to drop some. Instead there tend to be two underlying causes. The first cause is that the professor wants to reclaim the disk space used by the account because the other option is buying more disk space and they'd rather not. The second cause is that we've noticed some problem with the account (for example, email to it bounces) and the account sponsor decides that removing it is the simplest way for them to resolve the situation. This usually doesn't happen for recent accounts; instead it tends to happen to the accounts of people who left years ago.
(Account sponsors are 'responsible' for accounts that they sponsor and get asked questions about the account if there are problems with it.)
Our current approach to account removal is a multi-stage process, but it does eventually result in the login getting deleted (and sometimes that happens sooner rather than later if the sponsor in question says 'no, really, remove it now').