Hi,
In my shop I see the same issue of tax not being calculated on the shipping costs (anymore?).
Never seem to have had this problem as far as I now.
On my shipping I have a price, tax category etc setup but the tax is only added to the products in my cart, not the shipping.
Just to be certain I downloaded a fresh copy of Hikashop and updated my package but no luck yet.
Update : found that it's due to a tax rule behaviour that I cannot explain yet.
Should apply 21% on people who have no tax number but that did not had the desired effect. It removed the tax on all items with 21% tax ...
And because the shipping was also due for 21% tax it was also removed from the shipping.