Zero (0) quantities are shown for categories when they are displayed as a static 2-level tree.

1. Please make sure that 'Is Anchor' option for the root category of your store is set to 'Yes' (Catalog -> Manage Categories -> Root category -> Display Settings tab)

Magento Root Catalog

2. Reindex data. Go to System -> Index Management, select all indices and reindex them.

See more details on Improved Layered Navigation page
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