Yes, it seems that Mr Dark is a homage to Morpheus
From the Fables Wiki:
While Dark Man's name does not come from any specific story, it is clear that his presence carries out in various panels of literature, folklore and mythology, having collected names such as the Bogeyman, the Dullahan, the Khokhan, the Buse, Mörkö, The Dunganga, The Abo Ragl Ma Shokla, Burned Man, Lake Man, Buback, Torbalan and too many others to mention. However, he bares a striking resemblance to Sandman's Morpheus, and may have been based off of him.
Also in this article:
It’s a wonder then how little mention was made of the writer Bill Willingham’s wink and a nod to Fables’ influential “predecessor”, Vertigo’s “Sandman”. “Sandman” started off with it’s God-like main character freeing himself from the prison he’s spent a long time in and going on a quest to gather his items of power. [...] What has happened in “Fables” then, was that it’s creator, Bill Willinghem decided to have a massively powerful being awakened from it’s year-long confine and dealing with the beings that have usurped his power since.
And look at those two panels side by side:
But saying that he looks somehow like Dream of the Endless, those two figures have not that much in common: Morpheus is interested only in dreams of the mortals, very rarely enters our world for purpose other than to visit particularly interesting sleeper. Mr Dark as a contrast is attempting to subjugate the world, or at least the Fables living in this world.
Also, its worth to point that the Fables universe is totally separated from other DC/Vertigo comics, while many characters from "Sandman" interact with characters from other books - Death met Lex Luthor, Batman was at Morpheus Wake, Destiny met Superman etc.