Nikon's recommendations were always on the conservative side, meaning the hood should not vignette even if you put a thick filter on the lens and then attached the hood.
In the age of digital photography, filters are not that commonly used any more, and the sensor is sensitive to adverse effects of stray light (non-image forming rays). Thus the deepest possible hood is to be preferred. HN-3 is about as deep a hood as you can put on your 28/2.8 AIS. If the hood later gets knocked about and starts to lose its shape, it might vignette slightly. Thus, HN-2 might be a safer bet although you allow more stray light into the camera with that hood.