I'm not sure why you'd keep both '08 and '09 versions installed. '09 will save documents as '08 if you need to send that version to someone without '09.
If you double-click an '08 file, it
could be opened by
either version. Then, if you aren't careful, you could save it as an '09 version creating confusion the next time you specifically ask '08 to open it.
That's a common problem with any app that updates/changes file formats/capabilities of course.
Unless you absolutely, positively
need the '08 version around, I'd just uninstall it [all apps, not just Numbers, BTW] (and the pref file(s)). Then, re-install '09. A Restart might also help. Then, select any '08 document and do a Get Info on it. Change the "Open with..." to the '09 version and click the 'Change All...' button.
Second thoughts, prior to deleting the '08 versions, make an archive of the three apps and the registration info for them. Then store them on an external drive, DropBox, DVD, etc. You can't be too safe!