Game play-story segregation. Whatever Avernus discovered it's implied to be a big deal. I mean the dude is 300 years old. He wouldn't try to get missive to Weisshaupt unless it was urgent.
Not relevant to the topic though. Nathaniel didn't drink the same potion, and he's spent a lot of time around Darkspawn. There is nothing, in the games or in the EU to suggest that he ever met Avernus, much less drank the potion that the PC Warden did.
There was the events of Awakening and then in DA2 you see him again, in the Deep Roads, surrounded by darkspawn. The dialogue he has hints at more Awakened Darkspawn around, and that he's doing something for them. The more time a Warden hangs out around darkspawn, the faster the Taint progresses.
I'm not saying he's on his Calling. However, we can't dismiss the possibility that he's no longer alive.