Hi,
I don't see why you would get two emails. You should only get the activation email from HikaShop and the link there should work.
That's how it is on our end and for everyone else so far.
So I'm suspecting that you have some third party extension messing with the user registration/activation process.
If you go in the menu System>Emails of HikaShop Business, you can deactivate individually each email. So deactivate there the "user account" email and your customers won't get the HikaShop activation email.
Alternatively, you could also turn off the activation of new user accounts in the settings page of the Joomla user manager. Which would also help for the workflow of your checkout.