AF-D lenses went away without making much fuss. Some designs never made it into the AFS era, for example, the twin DC-Nikkors 105 & 135.
As long as manual focus works, I for one don't care whether the Micro-Nikkor lens in question is AF/AF-D or AFS as I never use these with AF anyway. Currently I have two (well-worn) copies of the AF-D 60/2.8 nd that'll do for now. Actually I prefer them to the longer 100/105/125 lenses for some applications, such as shooting verticals on my Multiphot stands.