Will Unity iPhone Demo Files Work on Unity iPhone Basic or Pro?

Yes, the files are the same from the demo and the full version of Unity iPhone. You shouldn't have a problem opening a demo project in standard Unity iPhone (Basic or Pro).

And no, your project directory will not "stay the same through the 3.0 update". Unity changes the way the assets and project folders are stored, so there is absolutely no backwards-compatibility. You cannot open a newer project folder in an older version of Unity. When you upgrade your project folder to Unity 3.0, you cannot open it in Unity 2.6.x nor can you downgrade/convert it to the Unity 2.6.x standard. This typically holds true for all Unity releases, not just 2.6 > 3.0.