I've come up with a somewhat interesting idea...
Eberron's hidden status in the Great Wheel is able to work largely because it is one world; one world out of many within the Material Plane should not be too difficult to hide, and escape the notice of several preoccupied deities.
But the Planes of Magic, or what
@dave2008 calls the Aether Realities, are many. There are something like 80
known planes. And lore says that although the number of planes is probably finite, there are so many it is impossible to count them all.
With such a high number of worlds, hiding all of these in one area would simply be impossible, and the "null space" of impenetrable area would be common knowledge, even if not understood, by the gods of the wheel.
So how does one hide countless worlds? By placing them everywhere.
Right now, Spelljammer lore has each D&D world in the Material Plane within its own Crsytal Sphere, that can be reached via Spelljammer. My suggestion is that each plane is also within its own Crystal Sphere; the difference, is that the Blind Eternities cloaks them all, spread out across the Material Plane like a web.
So there are the "known" worlds, easily accessed by Spelljammers and connected by Phlogiston routes. Then there the the "cloaked" worlds, or Aether realities, that are also spread out, but cloaked in the Blind Eternities. The cloaked worlds connect to each other through tendrils of the Blind Eternities, a web that connects the planes like nodes, a web that Planeswalkers access to travel between worlds. Planeswalkers also can't access worlds beyond the web.
This way, there is no big "null space" that the gods will easily see. Instead, there are much smaller cloaked worlds all across the Material Plane, each one going unnoticed.