Customization is always a trade off. Sure, if you want to do customize something precisely to your needs you might have to change one or two lines of php here and there. But HikaShop already allows you to customize a lot of things without having to see a line of PHP. And for the rest we provide an interface for it which will keep your modifications after updates, unlike other cart where you will loose your modifications each time you update.
The order number and the link to the order is indeed displayed by the same %s variable in the translation. If you want to remove just the link, you will have to edit the email file. That can be done in the menu System->Emails. There, by editing the order creation notification email you will be able to change the code
$url = $data->order_number.' ( '.$data->order_url.' )';
to
$url = $data->order_number;
Emails customization is only available with the Business version of HikaShop.