If you have not done so already, try the Library First Aid Tools.
Has the file size of your library changed, after the upgrade, or is it still big enough to hold all the images? Probably the images are still all there, but hidden or not linked to the projects.
Post back, if repairing and rebuilding does not help.
I had already tried to rebuild the library, but i could only do it through aperture 2
The Aperture 3 release notes strongly advise you to rebuild the Aperture library before upgrading to Aperture 3. See the link below. You have to scroll down a long way, before finding this piece of advice.
Unfortunately, most people discover that the Aperture Library is corrupted only after upgrading, and than it will be too late - tfor hen they have no longer the previous version of the program and a backup of the library, so that they can go back and rebuild the library before upgrading.