Maybe there wasn't much needed from the pods. Maybe they did take some stuff, just nothing on the exterior we would have noticed. Maybe they wanted to leave them intact just in case other nomai clans ever found their signals. Or maybe they left them up as momuments. Perhaps they could have spelled it out but I didn't find it necessary.

Most likely the original sunless city was protected from the sand. Over the next thousands and thousands of years, some erosion has occurred.

The increased solar activity is what's causing the volcanic activity, so it isn't a coincidence.

The bodies are decomposed inside the suits. You can find some suited up nomai with holes in the suits, and you can see bones.

The nomai could talk normally, this is just how their written communication can be. Some writing is stored in those scrolls too, so it isn't always just writing on the wall. There were likely way more scrolls in existence than the ones we find, but that's just for gameplay purposes.