There are several reasons why the updates don't show as free for those who already have iWork '09 installed.
1. You must have iWork '09 apps installed & they must be updated to the x.3 version. You can also download the standalone updater from this page.
2. If you are not using English as the primary language for your Mac, change to English & run Software Update. You can then switch back to your preferred language.
3. Go to Mac App Store (MAS) > Click on Store > Check for Unfinished Downloads. You will need to individually click into each application > Click update > enter in your Apple ID & password and then it will start updating.
4. Open App Store on your Mac & look at the buttons under Keynote, Pages & Numbers. If it does not say “Update” click Account under Quick Links, enter your password & click “View Account.” Next, click the “Reset” button to the right of “Reset all warnings for buying and downloading” at the bottom of this page, & click Done. Check your updates tab & iWork & iLife updates should now appear.
These are the ones I've seen work for others.