I have over 10,000 photos.
I keep about 3000 on the main computer and the rest on a B/U HD.
I did not think that was unusual .
I have the exact same set up for my iTunes and it does not remove the tunes if I leave it in library #2.
I have only the boxes check off in both iTunes and iPhoto that I want to sync with the iPhone.
I have an iMac with a 40k library. They're all on the Internal Drive. But that could as easily be on an external. By then end of this year it probably will have to be.
The iTunes Library (25k items) is on an external.
They sync with 2 iPhones, and iPad and iPod Touch.
I can see the point of having two libraries if you are using a Laptop, but as the desktop never moves...
Anyway, For more I'd ask on the iTunes or iPhone forums as they control the syncing rather than iPhoto.