Hi,
The warehouse system was a good idea, but indeed, it won't work for your needs.
Instead, the solution is to enable the "shipping price per product" setting in your shipping methods.
Then, in each product edit interface, you'll have a "shipping prices" section. There, you'll see listed all the shipping methods with this "shipping price per product" setting activated. So edit the products for which you want to remove shipping methods, and in that "shipping prices" section, add an entry with the "block" checkbox checked for all the shipping methods you want to disable when the product is in the cart.