Quickerer, the whole point here is that some of us don't want to have to manually close all windows before quitting Safari. For Numbers and Pages, re-opening windows is a great idea. Re-opening browser windows is problematic.
1) Sites with session specific URLs will probably fail to load, and expired sessions may prevent reloading anyhow without authentication
2) Forms may be resubmitted (although Safari will warn about this)
3) It's not cool to sit there while Safari frantically tries to reload a dozen web pages that I'm no-longer interested in. Local files typically open quickly, and are persistent works in progress. Web pages are typically slower to load, and more ephemeral then local files.
I'd be very happy to find a way to disable this for specific applications. Gaunibwe, what you suggested works only if the user deletes that folder each time before quitting Safari. That seems cumbersome. ag2web, the script you have there affects all applications or none, so it doesn't address the question at hand. Also, this isn't just about when shutting down the computer - it's about quitting and relaunching Safari, without it restoring windows.
You do have an interesting though; GUI scripting could be used to send a shift key press to prevent safari from restoring its windows. Kind of clunky though for the average user.