In Magento, there are things that matter and things that don’t matter.
Things that matter:
Adding things to catalog product, having all the information there and having it display in the intended store.
Adding things to Category Maintenance and having them show where you want on the website.
Things that don’t matter:
Cosmetic issues like whether the number in the parenthesis in the category maintenance tree accurately reflects anything in particular. The way it’s generated allows for an error margin, it’s only an indicator.