As Michael says, disable them. JIRA stores references to them in comments and history as their database id, not as text of their name so deleting the user will cause sql errors when viewing issues that would want to reference them. I move them to a group named 'inactive'
Are user ids unique for "system lifetime"? What I mean is, what if user A gets a user id X because of some internal naming conventions, leaves the Company and later user B would get user id X because the naming conventions lead to the same as of user A? Do you say "OK, A is not here anymore but user B gets a different id as if user A was still here"? Or does B get X and hence access to all issue A had before?
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