How to best design the entity data classes for the following SQL Schema?

Answer 1

If you modify the 'StoreProduct' table, so that it has no surrogate primary key, but a primary key which exists of the 2 foreign key columns (ProductId & StoreId), then you can simply limit yourself to 3 entities: - Employee - Product - Store

Your Store class could then have a Set of Products, which can simply be mapped as a many-to-many relationship.

public class Store
{
   public int Id {get;set;}
   public string Name {get;set;}

   public ISet<Product> Products = new HashedSet<Product>();
}

And in the Store.hbm.xml mapping:

<set name="Products" table="StoreProducts">
   <key column="Store_Id" />
   <many-to-many class="Product" column="Product_Id" />
</set>

So, to answer your question: first option is better.