It goes without saying there are spoilers.

While I have been a lifelong fan of Lovecraft's I had never read "Mountains" and just finished it. Towards the end the characters witness "a shapeless congeries of protoplasmic bubbles, faintly self-luminous, and with myriads of temporary eyes forming and unforming as pustules of greenish light" and I thought that sounds an awful lot like Hermaeus Mora.

Now we know why HM got a facelift for Dragonborn. Or at least now -I- know, I'm sure others already knew this.

So the Daedric Lord of Fate is, in fact, a Shoggoth. Trippy.

Well it's not really that Mora got a facelift, Daedric princes can change their appearance at will, Sheogorath has had a new appearance with each game. As for Herma-mora, he is very lovecraft inspired the specific being you're talking about is the Lurker beyond the threshold who is the common avatar Yog-Sothoth uses, yog-sothoth being a being of vast knowledge who transcends time and space and knows basically everything good ole' Herma-mora is heavily inspired by Yoggy. So yea, Herma-Mora looking like Lurker beyond the threshold was pretty much intentional