Actually, the problem is not that Aperture does not read the NEF files - it's that it SOMETIMES calls them out as unsupported. What happened to me 2 days ago was that I imported 300 or so NEF files while renaming - no problems viewing them all. I then ran the NEFs through DxO Optics Pro - a post-processing package that created JPEGs from the NEF files (leaving the NEFs untouched). Imported the JPEGs into Aperture - again, no problems whatsoever.
The following day, I returned to that Aperture project and started looking through the images - and that's when a bunch of them popped as unrecognized. The very same ones that were fine the day before. The very same ones that were fine after I quit and restarted Aperture, for that matter.
So this is not a case of not being able to read a format - I've been using APerture since v1.5 with this same camera and RAW file format - and certainly it shouldn't have any problems with JPEGs. And once I quit and restarted it, it was fine again.
So the bughas to do with this sporadic problem, which apparently is not something unique to my system.