Hi,
First, please note that the login module of Joomla is not part of HikaShop. If you're talking about that, or the login form page of Joomla, we can't help. You'll have to check on forum.joomla.org
I'll assume you're talking about the login form inside the checkout of HikaShop.
There are actually 4 different login form layouts in HikaShop.
Based on whether you have the "checkout legacy" setting activated or not in the HikaShop configuration the system will use two different view files. And based on whether you have the "Use bootstrap v2 design" setting ativated or not in the HikaShop configuration, the layout classes and HTML will change too.
So while I recommend keeping the "checkout legacy" setting turned off, regarding the "Use bootstrap v2 design" setting, you could try switching it. It might work better with your template CSS.