The "include" file is just a js file that document.writes your html, so its not easy to make edits because you would need to do it in a big stream of escaped code.
They won't work if user has js turned off.
They are awful for seo because the includes will not be there when the page is crawled
They are not semantic for writing things like <html><head> and will throw your browser into quirks mode because your page would effectively start with a script tag.
But I used the hell out of them back when dynamic hosting was hard to come by (geocities, tripod etc)
