Don't forget to backup your marks and highlights also. I made that mistake once, and then lost my Kindle. Lost years worth of highlights and notes, so now I set up a bash script to automatically sync them to a Git repo when my Kindle is plugged into my laptop.
Your bookmarks and highlights are synced to the cloud. You should be able to read them online on: http://read.amazon.com/notebook
From the kindle you can also export all the highlights of a book to your email. It's a lot better to read it on your email. The kindle device reader note reading experience is subpar.
Yes, but only for the books you purchase through Amazon. If you import DRM free books (or presumably re-import DRM free versions of Amazon purchases) or personal docs, the notes on those won't be saved.
Tangential, but is there a way to scrape this page or an API to access it? I'd like to be able to automatically pull my highlights and haven't found an easy way.