Hi,
This is not a known problem.
First, check the Customers>Emails history. Do you see the missing emails there ?
If yes, then the emails are being sent by HikaShop and the problem is elsewhere (in the email server of the hosting sending the emails for example).
If no, then check the menu System>Emails. There, is the "order creation notification" email still enabled ?
Did you customize it ? If you click on the "preview" button and generate a preview of the email for an order, do you get the email generated properly ?