Some of the websites you've been looking at almost certainly belong to a guy called Joseph Mercola (and others like him), who's making a fortune out of selling "health supplements" online (you can read more about him in this article:
[broken link removed - similar info can be found here: https://quackwatch.org/11Ind/mercola/] ). He's a clever guy - he bought his website domain back in 1997 when the Internet was in its infancy, so he got lots of other websites linking to his site over the years, and as a result his pages often come up first during Google searches (despite the quacky content).
Mercola (or his team) latched onto a book published in 1993 by a retired dentist called George Meinig, who was convinced that root-filled teeth cause many illnesses. His book was based on research in the 1920s by a guy called Weston Price, an American dentist and dietician. Price came up with his "focal infection theory", which alleged a link between endodontically treated teeth and broader systemic disease. Compared to modern scientific research, Price's research was rather haphazard (lacking proper control groups amongst other issues).
Price's theory fell out of favour in the 1930s (not until after lots of people had had their root-canalled teeth and tonsils extracted!). It seems to me that Meinig was a conspiracy theorist who was convinced that there was a massive cover-up of Weston Price's findings by the scientific community and his fellow dentists (hence the title of his book, "Root Canal Cover-Up").
Weston Price's research findings have never been replicated. Having said that, root canal treatment in the 1920s was pretty primitive and not sterile at all, so it wouldn't be all that surprising if some people did suffer from nasty side effects at the time.
In short - don't believe everything you read on the Internet

. There is almost always some commercial interest behind alternative health sites, and most of this involves selling "health supplements" (some of them decidedly dodgy).