Well, if you want to bring modern theology into a game. I guess. Atheism is a modern day religion. It's kind of like saying, will there be Buddhism or Christianity. That's just weird. Skyrim should have it's own religions entities.

Not likely. Atheism really only could develop as a belief after the development of science and accumulation of knowledge. In a world of magic, where advanced sciences don't really exist, its not likely atheism would exist either. Basically a belief in gods and spirits were a way to answer questions for which no answers could other otherwise be found.

On Earth, it was only after science could start providing some of the answers to these questions that people even challenged the existence of gods. If you go back 1000 years, there was no one who questioned the existence of gods. Sure, some hated them and were definant of them. Certainly, not everyone bothered to worship them or care, but they definitely believed they existed. That was the ONLY answers they had at the time for things they saw around them.

Back on Nirn, people don't have any scientific answers, only magical ones. They can witness miracles everyday in temples. The events that take place frequently PROVE beyond the shadow of a doubt that their are beings of great power in existence. I daresay that if a giant four-armed "demon" and a fiery gold Dragon just suddenly appeared over any major city on Earth and had an epic battle trashing most of the city and then disappeared, the number of atheists on Earth would drop dramatically overnight.

I just think it would make sense if more people, despite believing in the gods, didn't worship them. This was a big part of Dwemer culture (they stated that they "preferred instead their gods of Reason and Logic"), but of all the races that still exist, only a few people seem to question the gods.