According to the wiki, the Dracula X boss, who's official name is Ghost, is based on Shaft, but is not confirmed or even hinted to be him.
CotM Necromancer's first form bears more of a resemblance to Shaft than CVDX Ghost in that they both have the appearance of an empty cloak whereas the Ghost has skeletal hands. This and the fact he is visibly decaying makes me think he has more in common with a lich than a ghost.
Also given that Shaft's Ghost summons skeletal monsters the CotM Necromancer is more of an homage to Shaft what with his winged and horned second form. The Ghost on the other hand could have been more like Shaft but they chose to give his abilities to Anette/Carmilla instead.