Hi,
I see you have the "checkout legacy" mode turned on in your HikaShop configuration, so you're using the old checkout.
If you're updating from an old version anyway, I would recommend trying the new checkout system. It should work better.
Note that rather than copying the file from product, it would be better to just add such code at the top:
<?php $this->params->set('price_with_tax',0); ?>
I'm also not able to reproduce the issue with the payment fees, be it with the legacy checkout or the new checkout.
Wouldn't that come from an old view file override of the checkout/cart.php ?