There isn't information openly available about NSC, so what follows is quite a lot guesswork.
We think that applications from people who are nationals of, or have lived in, countries where there has been unrest and/or insitutionalized repression, get referred for these checks. NZ have a policy of not granting visas to individuals who have been personally responsible for any such issues. Therefore, they ask for a detailed employment history, and assurance that they haven't been in the military or other employment with the repressive forces. They have to wait for responses from the foreign regime, who do not give any priority to replying quickly, hence the long delays.
As when someone's medical is referred to an MA, the CO cannot grant a visa until after a favourable answer comes back.
However, the application still has to go through all the same checks as everyone else's - qualifications, work experience, partnership (if relevant). And there's no way to tell if a particular CO will have done all that part of the work while waiting for the NSC result, or whether some parts will still remain to be finalized.