I know this post was way back in October, but I just had this same issue. After reading the comments, I tried to update Aperture via the purchases tab in the App Store, but nothing happened. I called Apple support and they wanted $29 to help me, but I chose the option to talk to someone about buying the option for help, and told them my issue. They referred me to the Aperture help and I didn't have to pay anything. I had downloaded Aperture originally from the App Store. Those that have the disk, may have to do this a different way.
That being said, here are the steps they had me do:
1. Uninstall Aperture. Go to finder; applications, find aperture. Click on Aperture, and look above to Action, click on that and click on Move to Trash.
2. Open the App Store
3. Go to the Featured tab in the app store
4. Click on Account which is on the right side of the page. A box comes up for you to put in your password! Don't put it in.
5. Sign out.
6. Go back to Account, and sign in.
7. Go to purchases. You will now see Install to the right of the Aperture Icon
8. Install it again and the pictures will be there.
She gave me two pieces of advice.
1. Whenever you update to a new OS system, always check to see if there are any other updates you need for your apps. Update them first. If it says it needs the new operating system, that's ok.
2. Always do a time machine backup before updating.
I hope this helps everyone!