We're in one of those fun situations where the answer to your question is, "It affects most incorporeal undead, but not for the reason you brought up."
I brought this question to an off-site friend of mine who's been a D&D enthusiast for years, and he did some digging in old sourcebooks as well as the 3.0/.5 supplement Manual of the Planes, and according to what he found the two parts that need addressing are "What is an incorporeal undead's nature?" and "How does the Sphere of Annihilation (and the raw substance, Voidstone) work?".
All incorporeal undead are partially Ethereal, meaning that they exist on both the Ethereal Plane and the Material Plane (or any other plane that connects to the Ethereal, potentially). Annoyingly, this fluff statement is not backed up by hard mechanics, but it implies that an Ethereal being could damage an incorporeal undead without the need for further measures. The exception to this dual nature is Ghosts, who are Ethereal primarily but can temporarily manifest on the Prime Material plane. On the Ethereal Plane they have matter that's made of something, since Ethereal beings can touch and attack them freely, albeit at their own risks. On the Prime Material plane their 'substance' is somewhat more debatable, though it is a projection of their true bodies and can in some cases (such as the Ghostly Grasp feat) have enough substance to affect the physical realm.
Now, the Sphere of Annihilation differs from the raw material that creates it, Voidstone (which is detailed in the Manual of the Planes). Voidstone is a concentrated version of the Negative Energy Plane's relation to annihilation and destruction and has the potential to destroy anything that "makes contact" with it. Most Incorporeal creatures are incapable of making contact with it, since they're not all there on the Negative Energy Plane, but if they have the Ghostly Grasp feat or the Voidstone is brought to the Ethereal Plane it destroys them like it destroys anything else that touches it.
The Sphere of Annihilation itself is Voidstone that has been refined into a yawning planar gap that sucks beings, objects, and matter into itself. If you could imagine the multiverse as a series of fabric maps with threads connecting them (those are portals and planar connections), the Sphere of Annihilation would be a moving hole that leaves tears behind it. As a planar gap it is stated (but, again, no RAW so rule as you will) to affect incorporeal and ethereal beings, since an entity on the Border Ethereal (the part near the Prime Material or another plane) is close enough to be sucked into trans-dimensional effects such as the Sphere. However, it is of some relief to incorporeal creatures that the Sphere of Annihilation cannot be brought successfully into the Ethereal Plane proper, as any attempt to do so opens up an Ether Gap - a sucking hole in the raw potential that composes the Ethereal Plane that drops victims outside of reality entirely and incidentally destroys the Sphere in the process.
Citations - Manual of the Planes (contains information on Voidstone, the Ethereal and Border Ethereal, and the Negative Energy Plane), Dungeon Master's Guide (contains fleshed-out flavor for the Sphere of Annihilation). I'm asking my researcher about his other sources; if he divulges them I'll post them here.