Hi,
As I said, it could be that the user account email has been unpublished in the menu System>emails.
That could explain why you still get the joomla email but not HikaShop's.
Otherwise, it means it comes from the Emails settings of the HikaShop configuration and you should check that with your hosting company.
A simpler alternative would be to turn off the user account activation option of the Joomla configuration. That would remove a step from your checkout workflow ( and thus increase your sales ) while at the same time circumvent the problem and enabling you to use the normal registration, like before.