In the main series, it is said that the Hist "acknowledge" Sithis and the Shadowscale tradition is described. One of the novels refers to a Xanmeer dedicated to him called "Exact-Egg-Breaker" as I recall, which makes him sound like something of a creator deity rather like how the Dunmer who Sithis says that that the universe was nothing before it.

In ESO, I've heard that there's a fair amount of interaction with Shadowscales in the Shadowfen chapter of the game and an Argonian Dark Brotherhood sanctuary is visited. From what I've seen of the statue in the splash screen, it adds some much desired (by me anyway) savage exploitation flavour to the black-and-red-accented tone of the Dark Brotherhood, but it's not exactly sympathetic by contemporary moral standards and doesn't alone explain how it's all such an institution in Black Marsh. It also begs the question as to why the Shadowscale tradition ended in the 4th Era (besides half of everything being in decline as part of TESV's theme).

Try not to tell me with spoilers.

Possible Skyrim spoilers:

Besides the Hist, Argonians in general seem to venerate Sithis, and they do not seem to recognize the existence of Aedra and Daedra as gods/deities at all (Argonians do not "worship" and have no religions of their own, merely just rituals to honor the Hist and revere Sithis). There is mention of Z'en being venerated by some Argonian cultures at one time, but it's stated that practice ended, likely by cultural taboo. Largely it seems that the deal with Argonians and Sithis has to do with Sithis having connections with death and rebirth in Argonian culture.

I suspect a lot of that.

Shadowscales very much exist in ESO though. That means that if it is an Imperial institution, it isn't a Septim one like Morrowind's monarchy.

What's particularly striking is this:

"The vaults beneath the Sunscale xanmeers were built by a long-gone Argonian tribe in honor of Sithis, the "Dark Husband." They are said to contain tests for those who think to withstand the call of the abyss."

So far as we've heard otherwise, the "Dark Husband" figure of Sithis is unique to the Dark Brotherhood. So I think it stands to reason that either the Dark Brotherhood loaned Sithis the "Dark Husband" to Argonian tradition or Argonian tradition loaned Sithis the "Dark Husband" to the Dark Brotherhood. It seemed ludicrous to me that a Sithis anything like that could have a mainstream following, but I'd say same about Mephala and Boethiah if I didn't know better (although I very much doubt the Reclamation following Dunmer have dropped thousands of years of New Temple values for the old more Darwinist ones in a couple of generations).

With the connection between the Hist and Sithis, I would assume that Sithis in one form or another, has been recognised by Argonians since they invented mud. In the DB->Argonian scenario, it's possible that Argonians adopted the Night Mother embellishment after it happened where ever it happened. This would entail the Dark Brotherhood becoming an accepted and influential institution in Black Marsh.

In the Argonian->DB scenario, I suppose that the Night Mother is someone Argonians recognised first. Which is odd because her body looks nothing like an Argonian*. However she may have originated in a more human looking culture. There's no apparent trace of that culture now, but that would to be expected around Black Marsh as a lot of its old cultures are extinct (such as the Kothringi and that particular tribe that built Sunscale Strand). She could have been a Nede from Blackwood or the Nibenay Basin before her tribe and others were wholesale enslaved by the Ayleids.

Or maybe the corpse isn't the Night Mother. Maybe it's just a conduit to her. In this case she could anything, perhaps an Argonian mother whose remains perished and needed a replacement or perhaps she really is Mephala. There's no indication I've seen that Argonian believe this, but they're usually secretive and Mephala is a lot more secretive. She may have even given the Hist a reason to keep the secret from their own people.

I've said nothing about the Morag Tong, but I assume that the Chimer or Dunmer brought it to Black Marsh at some point, even if it was just among the Cantemiric Velothi. The Dark Brotherhood could be what the Morag Tong became when it went native, then spread and Westernised.

*That said, she also apparently unrots between TESIV and V. Either its a different corpse, the Keepers know some remarkable corpse restoration techniques or it was an aesthetic choice with no explanation.