1. For mobiles it's generally best to stick with "fixed size" option on the UIRoot for Android devices, as there are simply too many of them to do anything else.
2. No, prefabs within prefabs are not supported by Unity. I wouldn't create a prefab out of UI until I'm done with it, and I would only do it if the UI needs to be present in more than one place.
3. Debugging of what? You can see what the mouse is hovering over by enabling debugging on the UICamera for example.
4. No gesture controls. NGUI is a UI kit. Gestures would be a completely different scope. Many use another well-known plugin for that alongside NGUI.
5. You can break things up into multiple atlases, but doing so will result in more draw calls. It's best to keep one atlas.
6. LoadLevelOnClick
7. % of parent object -- no. Parent object must have a scale of (1, 1, 1). % of another widget -- yes using UIStretch. Best to limit the usage of UIStretch however. Performance reasons.