Just about went crazy when there were no products in our categories and subcategories. Looked at everything in admin, and all looked good (everything published!). Then came to the forum and found there were many, many others with the same dilemma. Well, since I am such a newbie, and know virtually nothing about changing the code, piecing together what everyone else said, for the categories and subcategories with no products in them (ex. books (no products), hiking books (no products) local hiking (products), I just added a product from another category (ex. compasses and hiking maps) as products that the customer might be interested in purchasing also, something like "relate products". And lo and behold!! I had my categories with products in them back. This might not be the correct and proper fix, but we have our site back. Implementing this strategy might be the solution for those of you out there, like me, that only know the basics!!! Hope this helps.