I'm not saying the Matoran knew the true nature of their universe, but they are aware that Mata Nui watches over and protects them. They believe he is the stars above them, the ground they walk on, and relatively all-encompassing. They are also aware of the Great Beings, and that they had a hand in creating Metru Nui as well as presumably many other lands.
The Matoran's single-minded devotion to Mata Nui is an interesting point, one I'd be interested to learn more about. What is the "Matoran condition"? How are they content to work for thousands of years without exploration, without learning about the Universe around them? The Matoran are certainly smart and deductive enough to figure out the nature of Mata Nui, if they felt so inclined. But for 100,000 years they do not. It's rather curious.
As for the situation on Spherus Magna, you make some interesting points. I feel that upon the rise of the Great Beings, some, what? 265,000 years ago, if I remember? Upon their rise, I feel that religion would have ceased to be so pervasive in favour of secularism (if the Great Beings' mindset could be compared to a modern day materialist or scientist), as opposed to simply replacing whatever god(s) existed prior. As an aside, Annona couldn't be the only being older than the Great Beings; Spherus Magnan lifespans endure far over 100,000 years. If the Great Beings are in fact Glatorian as is claimed, they would have been simply the result of years and years of evolution (I'm comparing Spherus Magnan history to human history because it's my only reference; perhaps they could have come about in some other way, but evolutionary origins required the least assumptions), and there was probably a long history prior to the rise of these scientists. Now, the Glatorian and Agori probably treated the Great Beings as something beyond comprehension- maybe even supernatural on occasion- but I cannot picture the Great Beings proposing the people of the world blindly place their faith in them.
Upon the Shattering and subsequent disappearance of the Great Beings, religion definitely could have come back into popular belief. They were gone, and, as the mad Great Being once said, the people of the world will fill in what they believe them to be, creating their own unique image of the GBs. 100,000 years of hardship and starvation probably lead some to believe some long-abandoned God was punishing Spherus Magna for it's rejection of them in favour of these Great Beings, or something similar.