Spoiler Killed off when the Empire did its clean sweep of every single sanctuary in Tamriel.
But what about the Shadowscales serving the King of Argonia? The Mede Empire hold no influence there, so they could still flourish there. Maybe they found new masters?
That's not really the impression I got from reading the novels. The Hist had a very present influence on the ordering of Argonian society. The An-Xileel (sp?) were a unique political/social group of lizards because the Hist tree where they were at "went rogue."
The Hist are the only thing I imagine that unites the Argonian villages/tribes. The Hist have a huge amount of control over the Argonians, like mind control and hive-mind stuff.
My impresion though was that the the An-Xileel was the leading party of the country, the ones who listened and did the will of the Hist. So technically the Hist controls all, but the An-Xileel still employ assassins, in this case the Shadowscales, for more intricate political manners, something the Hist couldn't care less about. Positions within the Priesthood (what I understood them as) of the An-Xileel is a matter of politics and intrigue.
From the novels, it also seemed that the An-Xileel held a certain power over the Hist, by the way they were able to cut Hist-trees off from the network and make them go rogue. The Hist might be highly intelligent sentient beings who give Argonians their power and their minds, but they're not all-powerful. What if the An-Xileel dictates the Hist to do things while at the same time crediting the Hist and pretend to be acting on their orders? What if the top-tier of the group have "hacked" into the network of the Hist and control them to contorl Argonia? This is only speculation, but I believe the An-Xileel to be stronger and more influental than they want to let us know.