Not really a Perl question, but...

Stores have Inventories. Inventories consist of Items (I'm deliberately ignoring weapons and armor). To reduce/eliminate redundant data (in broad brush terms), you'd want a table that holds info about indivdual stores. You'd want another to hold info about individual items. You'd want a third to hold inventories (store_id, item_id, quantity).

Check out some books on Data Modeling and/or Normal Forms, or Google for it. Its a very worthwhile subject to understand if you want to do db work. At least until OO databases start becoming more dominant, if they ever do.