Hi,
I tried it here with the same setting ("Both"), on an order with a product at 100 € + 6 € of tax and 10 € of shipping without tax. The status notification shows:
Subtotal: 106,00 €
Shipping: 10,00 €
TOTAL without VAT: 110,00 €
TOTAL with VAT: 116,00 €
In the email, the product lines and the "Subtotal" line include tax. The "TOTAL without VAT" line is the whole order (products, shipping, payment fees, minus the coupon) without any tax, and the "TOTAL with VAT" line is the same with tax. As the shipping is added in the "TOTAL without VAT", that line can be close to or even higher than the subtotal, which makes it look like the tax is included when it is not.
If you prefer to see the tax amount itself instead of the "TOTAL without VAT" line, you can turn on the "Detailed tax display" option in the HikaShop configuration: the email will then list each tax with its amount before the "TOTAL with VAT" line.
If your amounts don't match that logic, could you post a screenshot of the email along with the details of the order (product prices, tax rate, shipping and coupon) so that we can check it?