Many-to-many relationship with a one column ‘junction’ table?
I would include the table you're calling @stock_stockForShop (though I might change the name to something like @stockpile or even @warehouse if that actually makes sense in context.

A stockCode represents a unique entity in your schema; it defines a set of inventory that is available to a set of stores. If you do not store it and enforce it as a foreign key, you have to allow new codes to be created via @stock and @stockForShop, meaning that a typo could create a stockCode that is not used anywhere else, leaving the associated stock to potentially go to waste. This is, perhaps, the most important point - ensuring that all stockCodes are well established and usable, and that new ones are only created deliberately.

In addition, a stockCode might also have important attributes that you might want to be able to search on from an application: it could be tied to a specific geographic location (such that it would make sense to connect to shops within 100 miles of it, but no farther), or contact info (phone/fax/email).

So, I would have the @stock_stockForShop table, and would make IDs referring to other tables as foreign keys (again, making sure that typos don't create virtual new stockCodes).

Terminology note: I would consider @stockForShop to be your linking/mapping table (which is how I read "junction"), as it ties a shop to one or more warehouses, and a warehouse to one or more shops.