Hi,
There is indeed no option to restrict custom order fields based on the shipping method selected.
The simplest is to have the fields not required and to modify the "fields" file of the "checkout" view via the menu Display>Views to skip their display based on the shipping method selected.
For example, with such code at the top of the file:
<?php $app = JFactory::getApplication();
if($app->getUserState(HIKASHOP_COMPONENT.'.shipping_id') == XXX) return; ?>
where XXX is the id of the shipping mehtod for which you don't want to display the fields.
If the fields are to be required, it's more complex as the system will refuse the validation of the step where the fields are normally displayed. So it would require a developer to help you with that customization.