If that is what you want then you dont really need multi-shop system, you can just as well have several different shops.
But if you still want to use the multi-shop system you can simply make the same product for each of the shops, then stock will be subtracted from just that store product. (ie. if you have 4 multi-stores you add the product 4 times and assign 1 of these "copies" to each of the shops)
Or you can custom code up a new stock system.....