To edit the shipping and payment buttons, you have to edit the views "checkout / shipping" and "checkout / payment" via the menu Display > Views.
Then in these views, you can revert the check on bootstrap when displaying the buttons, the code in question is:
<?php if(!HIKASHOP_RESPONSIVE) { ?>
<td>
<input class="hikashop_checkout_shipping_radio" type="radio" name="hikashop_shipping<?php echo $shipping_key;?>" id="hikashop_shipping_<?php echo $rate->shipping_type.'_'.$rate->shipping_id . $shipping_key;?>" value="<?php echo $rate->shipping_type.'_'.$rate->shipping_id . $shipping_key;?>" <?php echo $checked; ?> />
</td>
<td><label for="hikashop_shipping_<?php echo $rate->shipping_type.'_'.$rate->shipping_id . $shipping_key;?>" style="cursor:pointer;">
<span class="hikashop_checkout_shipping_image">
<?php } else { ?>
<td>
<input class="hikashop_checkout_shipping_radio" type="radio" name="hikashop_shipping<?php echo $shipping_key;?>" id="hikashop_shipping_<?php echo $rate->shipping_type.'_'.$rate->shipping_id . $shipping_key;?>" value="<?php echo $rate->shipping_type.'_'.$rate->shipping_id . $shipping_key;?>" <?php echo $checked; ?> />
<label class="btn btn-radio" for="hikashop_shipping_<?php echo $rate->shipping_type.'_'.$rate->shipping_id . $shipping_key;?>"><?php echo $rate->shipping_name;?></label>
<span class="hikashop_checkout_shipping_price_full"><?php echo $price_text; ?></span>
<span class="hikashop_checkout_payment_image">
<?php }
You just have to remove the "!" in
if(!HIKASHOP_RESPONSIVE) to not use the bootstrap buttons.
Hope this will help you.