This should be a simple question...
Do I need to run Adobe Customization Wizard every time on each new incremental reader update, or just once per major revision (e.g. Reader 9, Reader X)?
This question hasn't been answered because it would be better asked in the enterprise deployment forum. The Wiz is an ent deployment tool and only is used for initial deployments in most cases. You use it to customize the installer and the product when it's first installed. You could use it for any install, but that is a less common scenario.
Usually, you customize the first version you install and then just apply updates as they are released.