I'm 99% certian that shop order emails are sent once the checkout is complate and that they do not rely on the notification cronjob.
Are you able to send email from the system at all? Try the tipafriend functon to check.
http://yoursite/content/tipafriend should bring up the tipafriend form. Try send it to yourself. if you don't get an email then check the ez debug and/or the mailserver logs.