Hi,
You're almost there.
You will have to use the "warehouse" system of HikaShop that was added in the 2.3.0 release.
Create two warehouse and assign the first type of products to one warehouse and the others to another one.
Then, assign your two kinds of shipping methods into the corresponding warehouses.
Now, you will have your products grouped by warehouse on the shipping selection area of the checkout, with one shipping method to select per group and the total shipping amount will be the sum of both groups (if you have products from the two warehouses at the same time in the cart of course).