Your question reminded me of a post someone made here about a year ago. He was asking for help with his project, he shared a capx which was ~1Gb in size, and all objects were named like Sprite157 and Text93.
So yeah, don't be like that guy! Careful planning and good organization is crucial in a big project. But since you are asking these question, you know this already :)
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Making objects invisible when they are off-screen is not a bad idea. I don't know if this has been optimized in C3, but in C2 this helped to improve FPS and CPU usage by about 20-30% in one of my projects. I should mention that there were lots of effects applied to those objects. Also, where possible, disable behaviors and collisions for objects that are off-screen.
9patch has lots of limitations, I definitely prefer TiledBackground.