Regarding Ny'alotha, I have many wild theories. Hold on to your hats because it is ludicrously wild speculation time.
We start with Whispering Forest.
Whispering Forest is a zone in WoW with a few easter eggs and a very unsettling atmosphere. One of these easter eggs is a mushroom circle that will occasional be surrounded by fey dragons. The little guys will cast some sort of spell and sing a strange song. This easter egg implies a connection between Whispering Forest and the Emerald Dream.
This place is also likely where the High Elves first landed upon the Eastern Continent created by the Sundering. Some force is known to have driven some of the elves insane and caused to them to flee north where they founded our favorite city of pointy eared pretty people.
This force has been confirmed by Blizzard as something other than an Old God. This revelation leads me to another location in Wow's lore.
Chamber of Krasus
This chamber is likely located beneath the Whispering Forest in an underground citadel of mostly high elf and a bit of unknown architecture. The chamber, within the deepest part of the citadel contains a mysterious pool. When looking into the pool, Krasus often saw strange things at the edge of his perception. These things seemed to be creatures with very peculiar features. "When he stared into the pool, he saw odd shapes, which were at times "silvery fish," and at others still, a human torso, legs, or arms."
I always thought this was interesting but never thought much else of it because the scene was from a novel and possibly not canon. That is until I soloed Ulduar for the first time.
Within Ulduar there is a part of the raid called "Descent Into Madness." Within the Descent are many strange stained glass windows lining the walls. The first windows show what look like tad pool/humanoid babies. As you progress through the descent, the images change to show aquatic humanoids and eventually beings that are most likely Old Gods.
If the Whispering Forest has a connection to the Emerald Dream and the pool in Krasus' Chamber is connected to the Old Gods...I'm lead to believe that the Old Gods and the Emerald Dream share a yet to be revealed connection that goes much deeper than N'zoth or the Emerald Nightmare.
The answer might be contained within Ny'alotha/the Black Forest.
My current theory is that something very old at the center of Ny'alotha is not only connected to the Old Gods but possibly responsible for bringing them to Azeroth and/or spawning their corporeal forms and it has some connection to the Well of Eternity and also the pool within Krasus' secret chamber.