Disabling accounts programmatically I want to disable user accounts programmatically inside hook_cron() after a synchronisation job. I don't want to delete the users because of their generated content. But they should not be able to log in and receive any notification-mails and stuff like that.

Should I use the user status field for that? And if so should I use user_save to change this as I don't want drupal to send out mails to the users (via _user_mail_notify inside user_save) or just set the status fields inside the db? Are there any other hooks or functions that I would miss doing that?
Updating status through user_save() is a good way of doing it. 

Also note that when you set status to a value different from 1, $op will get set to 'status_blocked', for which no email will be sent.