How to know what percent of document that I read in Safari?
If you initiate a scroll a little bit either up or down a scrollbar will appear in Safari letting you know where you are in the document unless it has been disabled by code in the website.

You could use a "User Style Sheet" to have the scrollbar always appear: http://webdesign.about.com/od/css/ht/htcssusersafari.htm

Or you can do it the easiest way and go to "System Preferences > General" and choose "Show Scrollbars > Always".