Hello!
I've been playing a female dunmer sneaky sneaky thief, and decided for the upcoming DLC that I wanted her to be my vampire lord. So I decided to find a vampire and become contracted with Sanguinare Vampiris. I did, and went around doing quests (notably the Thieve's Guild quests) until I reached the end of the 3 day cycle. Yay, vampire! But wait a second, where has my scalp gone?

That's right. My scalp was gone.
Turns out that wearing the Thieve's Guild Armour hood or Linwe's Hood not only make the hood invisible upon equipping, the top of my hair (where I assume the hoods clip through the hair or it is removed on the hood model so it doesn't show through the back) is missing along with it.
At the moment this only appears to happen with Linwe's Hood and the Thieve's Guild Armour hood, and it only happened after I became a vampire. I assume that the same will happen if I equip another hood item that uses the same hood model, but as for different hood models such as the Dark Brotherhood hood, I haven't tried yet. I will edit this post with a list if I find a lot of other hood models do this as well, or any headpiece for that matter.