With Aperture 3.4.5, when I show the list of keywords, it shows me a count of '58' images next to one of them. When I create a smart album that simply selects that keyword, it comes up with 8 images.
Where are the other 50 hiding?
And the answer is: because some of them were sitting in the trash can.
I just struggled with the same problem, and I came up with the following possible causes:
The last part, images in shared services, also did give another symptom. When switching library, Aperture reported that my library contained approx 1150 versions. But if I opened 'Photos', there were only 700+ versions. So the last 400 were images located in photostream and on facebook, and some of the images in my photostream did contain keywords.