@Naeem - I'm still using 2.0 beta2, haven't upgraded yet to 2.02 but I will do it soon.
@splashingpixels.com - I tested this functionality on a test site that only had a clean WP 3.5.1 install, the twenty twelve theme and WooCommerce 2.0beta2. Still no order related e-mails being sent. The only ones sent are stock notifications (besides standard WP e-mails like new users, password reset etc.).
What I forgot to mention is that I don't use PayPal as a payment method, but just COD (Cash On Delivery) and Bank Transfer. I think this issue doesn't appear for those who use PayPal or other payment gateways.