Given that with NX the default is always to save as NEF, even after having made every possible adjustment, I'm pretty sure that NX works entirely on RAW data.
I would not be so sure about it. Remember, NX saves in the NEF file all operations as metadata - actions to be interpreted by NX itself the next time you open the file (similarly to what other so called 'metadata' converters - editors do). No NX modifications are visible if the NEF is opened by another NEF aware program (e.g. ACR etc).
Additionally, NEF is a very flexible format (much like DNG is). You can save de-linearised and de-mosaiced data (RGB) in a NEF file. In fact in NX you can open and 'modify' a jpg/TIFF file and then save it in NEF. That, of course, does not mean that the data is 'de-converted' to raw when saved in the NEF file. Do not confuse the file format with the nature of the data it contains.
So, the fact that NX saves as NEF does not tell us anything about the space NX operations are performed in. I'm pretty sure that all but some of the base adjustments are done on de-mosaiced data. I speculate that all adjustments which are supported for both NEF and jpeg / TIFF files are the same and operate on 'converted' data.
It is my speculation only but I think it is reasonable to believe that Nik Software took the Nikon converter engine and build their own RGB metadata editor on top of it to produce Capture NX. It would be easy for them to take another generic converter engine and do exactly the same producing a camera-independent NX product if their agreement with Nikon allows it.
Coming back to Aperture, the fact that a functionality is built-in in Aperture (or any other metadata converter / editor) does not mean that the function is necessarily performed on raw data. In this sense, it may not be different than performing the operation on an external 'destructive RGB pixel-editor' (like PS) as long as the bit depth and colour space is maintained. Of course, integrating the functionality provides all the workflow convenience of 'non-destructive editing' metadata editors are good for.
Unless companies document their products properly there is no straightforward way for a user to tell which operations take advantage of the raw data and which operate on RGB. It is true that in many cases this distinction may not matter much in terms of output results, but there are some (e.g. noise processing) where it seems it does.