Hi,
First, I would recommend to check to menu Customers>Emails history
There, you'll see the emails sent by HikaShop.
So you can check if you have the emails twice there or not.
If yes, then the emails are sent twice by HikaShop, if no, then the emails are sent once by HikaShop and they are doubled by the email server for some reason (maybe the receiver email address is twice in the email ?).
Then, I would recommend to check the "history" area of an order with the issue.
There is logged each modification of an order. If you see two emails in the Customer>Emails history listing for the order, it's highly likely that you'll see two lines of confirmation of the order by the payment plugin. This will indicate that the payment plugin has been called twice by the payment gateway to notify it of the payment (this can happen if he doesn't reply adequately the first time). And in that case, what that means is that the plugin should have some failsafe to not confirm an order that is already confirmed.
So you'll have to check with the developer of the plugin regarding that. Maybe they actually have a new version of the plugin and you just need to update it ?