What are your preferences for preparing the jpeg previews used by aperture?
i.e. are they compression artifacts because of the severe down scaling or compression in your Aperture previews
I'm away from my mac at the moment (in a world of windows at work) or I'd suggest where to find them, but you can define the properties of your previews to suit your workflow.
In principle this is not the cause of your problem because using the loupe should force that part of the image to be re-rended at the loupe's settings (I usually use 100% or more to avoid scaling issues in the loupe) but its worth you tweaking those to you personal favorites in any case.
Sounds like Nik is somehow adding the artefact to the preview it must give aperture rather than this being an Aperture alone issue.