How do I update Number '09 through the App Store?

The App store has no knowledge of your purchase of the physical install disc. You can use the the menu item " > Software Update..." or go here to manually download latest updater:

http://support.apple.com/downloads/#productivitysoftware

What version of Numbers do you have now? If Numbers 08 then your only option is to purchase Numbers 09 for $20 from the App store

iWork '09 installed from the retail disk or from the downloaded trial must be updated through Software Update. Those installations will not be recognized as installed by the Mac App Store. In Mountain Lion Software Update has been "rolled into" the Mac App Store. Choose Software Update from the Apple menu just like you always have & the Mac App Store will launch. Depending on what you have that needs updating you may see two sections in the MAS window.

But, as always, if you're not running the latest versions of the iWork apps installed from a retail box or the downloaded trial & Software Update says your software is up to date, make sure the applications are where the installer initially put them. The updaters are very picky. If the location is not where the updater is programmed to look or if the folder doesn't have the name the updater looks for, it will not work. The applications cannot be renamed or moved. If you installed from the downloaded trial or the retail box, they must be in the iWork '09 folder in Applications. That iWork folder must be named iWork '09. If it doesn't have the '09 Software Update won't find them & the updaters won't work.

You can also download the standalone updater from this page.

You may want to run Software Update again. There was an update just a couple of hours ago to iWork 9.3 that adds compatiblity with the updated 1.7 iOS versions.