For example, if I have a MovieClip with a ton of nested MovieClips and graphics on various frames ranging from 2 through 9999, but my clip never goes past frame 1, do those unseen clips cause a performance hit, or will Flash simply focus on what's being rendered onscreen on the current frame at one moment?
The unrendered content imposes overhead in the sense that it is included in the SWF, and thus is written into memory where the SWF itself is in memory. But I've never known such content to cause any other kind of performance hit.
It might be helpful to think of the stuff on frames 2 and beyond as class objects that haven't been instantiated yet. They don't impose any overhead beyond the class definition existing until you move the playhead to frame 2 (which is when any content on frame 2 is created).
Flash will simply focus on what's being rendered onscreen on the current frame. I have developed with some fairly performance intense animations and in parts on older machines it would slow down but only where the actual intense scenes occured. I know that all the actionscript in a frame get compiled into a function for that frame and so only execute when that frame is called so it makes sense.