So you're saying that you have two webites, a slave and a master.
If you're using jms multisites for that, then you should be able to configure different tax rules for different websites and in that case there is no problem. Each website will only see its tax rules and thus calculate the taxes based on its own rules.
I would recommend to contact the JMS multisites support in that case for how to configure that exactly.
If you're using another solution, then I don't know how that can work but the principle is the same. If the multisite system doesn't allow you to have different instances of a table (hikashop_taxation here) like JMS, then one solution could be to add a new column in the table hikashop_taxation in order to say which rule is for which website, and then modify the query which loads the tax rules in order to add a condition on that column based on the current domain name.
The query to modify is this one:
$query = 'SELECT b.*,c.* FROM '.hikashop_table('category'). ' AS a '.
'LEFT JOIN '.hikashop_table('taxation').' AS b ON a.category_namekey=b.category_namekey '.
'LEFT JOIN '.hikashop_table('tax').' AS c ON b.tax_namekey=c.tax_namekey WHERE '.implode(' AND ',$filters);
$this->database->setQuery($query);
in administrator/components/com_hikashop/classes/currency.php