Since iPhoto and Aperture use the same library format now, do you see your missing photos when you open the same library in iPhoto again? Did you upgrade both Aperture and iPhoto? Have you checked to see if you've entered any text into the various search fields in Aperture? Have you checked for any hidden search filters?
As for transferring digital photos, when you say it's difficult, do you mean that the process is complicated, or that there seem to be actual problems transferring the images?