Harold Saxon had designed and deployed the Archangel Network, the Valiant, and other things that were a matter of public record. And presumably people in the know (like Naismith, who had purchased Torchwood artifacts and records) had some inkling that these weren't just impressive technological feats, but probably beyond present-day technology.
Also, Harold Saxon claimed to have been in communication with friendly aliens who were offering us technology. While most of the world probably thought this was a hoax or a delusion after the Year That Never Was got rolled back, hints to the contrary probably existed in Torchwood files.
Then there's his close association with UNIT, which again would be meaningful to someone in the know.
Finally, it's possible that the Disciples of Saxon leaked information to Naismith to further their plans (just as he was clearly using them to further his plans). There were at least hints that Naismith knew Saxon was actually an alien, if not flat-out statements.