We see the chunk of Ven's heart that would eventually be turned into Vanitas be swallowed up by darkness before Vanitas himself emerged in a fetal position. I reckon that Vanitas's body is made of darkness, though how that happened exactly isn't clear.
Vanitas has Sora's face because Sora connected to Ven's fractured heart filling in the gap. Vanitas taking on Sora's face has something to do with a second hand connection that happened when Sora occupied the fracture because that's were Vanitas emerged. At least, that's my understanding of it.
I consider Vanitas a sort of "ani-human" if that makes sense. The Unversed get their name because "they're not well versed in their own existence" and "are the opposite of human life". Vanitas is the same to a broader extent, an empty creature made of darkness, born of fear, and nurtured by negativity. He has no desire for prosperity of any sort and even his self preservation is questionable.
All living things have light in them, even people like Xehanort and Maleficent and they're the scourge of the universe. As such, they have some willingness for improvement, even if it's just for themselves. Vanitas on the other hand seems to have no desire other than to see the world burn just because he can make it happen. He's all Thanatos and no Eros, lacking a speck of nourishing light that motivates everyone in some shape or form to preserve or improve positively.