I have a theory about all of this... humor me.
Akasha approached the pyramids in a very concrete manner. She took each piece of paper, and looked for the physical Book of Principles. On the pieces of paper was nothing (or perhaps... something hidden, but who is to say, I've never seen them), and furthermore when she saw they were blank she refused to accept the obvious lack of physicality of the books, and proceeded to write them herself.
Alche took a slightly less concrete manor, realizing that the pages might be a red herring or perhaps have deeper than face value. He, however, still believed in a concrete book, only this time he took a less concrete path. By entering the middle pyramid and imagining he was in the fire, he was, although what he found came close to the truth of the Book of Principles, it was not fully realized.
The Cube carried by Knator Commander was another such physical presence, and in my opinion, another red herring. The Cube itself holds no power, the power of suggestion, rather, is what attracted the Shades. Knator Commander believed they held something important, and so as a result the Shades believed they did as well.
Continuing on this path, let's think for a moment of the Golemus Wizard, who claimed that there is no Book of Principles. Akasha, of course, could not believe this, and as a result began making his claim false by creating a Book where there was none. However, I think the Wizard stumbled on to the truth.
There is no physical Book of Principles, just as there is no physical form of love, innately given to this world. The Book needs to be created or imagined, but to search for it will lead only to nothing. The Book exists somewhere on the Mount because we all imagine it does, and it will exist within the hands of an adventurer when we all believe that he possess the book.
This tale of the "second cube," I believe, is another such thing. The Shades were sent after the "Cube" that Knator Commander had for one of two reasons. One, they believe along with Knator Commander that the cube holds a deep secret, or two they realize that the true power of the Cube is not the Cube itself, but what it represents.
Therefore, it would make sense that the Shades do not need the Cube, the Book of Principles, or any other such item, because it is not the item from which power comes, but from the individual and the idea formed within the individual (often inspired by the item). Although it is likely that the Shades would want to give the Illusion that they are indeed after the Cube so as to keep the Myth of the book alive and running, and to let it hide the truth. The Book of Principles holds power because of the Principles it represents. If you understand the Principles, you can control and change them. If you can control and change them, you possess in your hands the Book of Principles.
Do I make sense?
Awi