I am experiencing the same issue. It is completely random and very irritating. I open Aperture up and go to import photos from my Canon 5D Mark IV in both JPEG and RAW and have the issue come up with only a few images available. Quit, run the import window again, get more images or sometimes none at all. Right now I'm in another Aperture library with a Canon S120 with just JPEGs and it doesn't see even one image. So there is nothing to import. Normally I just quit and restart Aperture over and over again until it finally registers the whole card, or just import it in batches if some show up and others don't but do later. But this time there is nothing no matter what I do. More on that later.
Here is the catch for this whole issue: Aperture is seeing it and processing what is on the card fully (the Activity window shows this) but it doesn't show up in the import window when it is processing the card like it normally does. Then after Loading Assets is done, it runs through the faces within a few seconds and goes blank with still nothing to import. The contents of the card has never been imported. This isn't a preference setting or any other setting. Here is a screenshot of my Activity window:

I have tried using Disk Utility to create a read-only disk image of the card and import from there but it is still the same. No photos for my current problem. It is completely random with no rhyme or reason. It doesn't matter the camera or how many photos are on the card, thus far. I normally have larger cards with a large amount of photos and/or videos.
I am running Sierra 10.12.6 and the latest Aperture 3.6. Going to try restarting the whole computer and see if that helps at all.
Everything else with Aperture, that I use anyway, works fine. Just this importing issue!
I'm starting to think it has something to do with the latest security updates over the last few months or something like that. The odd time it works perfectly without an issue but that is rare and was then and this is now. 😉
Under 10.11.6 it never had an issue.