"notesAdministrationProcess.DeleteUser" won't touch the vault. Domino does not have any API that can be used to delete an ID from the vault, or to mark an ID in the vault inactive. An admin must manually delete/mark inactive an ID entry in the vault. In the Admin client (Domino Administrator), if an administrator manually deletes a user, there's also an option in the UI about what to do about the vault entry. If the person is to be programmatically deleted, the programmer must take action to delete the entry in the vault.
Please allow notesAdministrationProcess.DeleteUser to have the same option for about what to do about the vault entry as the Admin client.