I can understand the concern. But at the same time, if you look at the direction Apple went with iTunes 10, I think they took it too far and nearly every review I've read thinks it's a turn for the worse. Previously, Apps, Movies, TV Shows, Podcasts, Audiobooks, Playlists, Playlist folders etc. all had different colors. It made it really simple to jump to that section without having to look closely at the icon or read the label. Now in version 10, everything is grey. Not great for usability.
What I envisioned was something very simple, a color density change for notebooks stacks, so you could see at a glance whether you're looking at a treetop or an individual notebook...
Colors in the Notebooks section are already used to indicate different state for the same types of objects: local (blue) notebooks, synced (green) notebooks, conflicting (gray) notebooks. It makes sense that if new colors are introduced, they are used to indicate states too, not different kinds of objects.
Also, if you have a long list of notebooks, you will only notice the color tone difference if you see a stack and a notebook at the same time (color tone differences are very hard to detect without both tones appearing at the same time). At that point, the indentation already tells you which is which.
That said, I found the notebook and stack icon shapes too similar, and had the same problem of confusing them. Since the stack icon looks so much like a normal notebook icon, I even (wrongfully) assumed stacks would have notebook-like behavior, such as containing notes.
I have a suggestion: how about 3 smaller notebooks instead of 2 notebooks? In MacOS X, they do this for the multi-documents icon (used when dragging):
They probably use 3 papers instead of 2 because they use this icon to differentiate between dragging 1 and dragging multiple files. Using 3 items makes the icon a wide rectangle instead of a tall rectangle, which is a more significant shape difference and easier to identify than the current "tall rectangle vs. a bit wider tall rectangle". Shape differences are very good for quick identification of things, so I think that his would do the trick. (I believe that is why shape is used to transmit the quick-reaction-critical message in traffic signs: STOP, YIELD, DON'T ENTER, INFO, while color is more of a secondary "degree of criticalness" message).