Saavik has these answered pretty well.
1. More or less what Saavik said. The individual cities are pretty independent in terms of governing, but dependent in terms of trade. Some of them, such as Chaduk Haven, only exist out of necessity for travel and trade, and are probably largely supported by trade organizations and wealthier independent traders. Others, such as Martis, are established because of their proximity to natural resources.
2. Yeah, not likely, although you might see some cultish types and spiritually-motivated tribal types. I doubt there will ever be any allegories of the Catholic church or anything like that in Aethora. Any spirituality in Aethora probably arises from the mystery of ather (you can have a good storyline with elements of spirituality without necessarily needing one or more gods and churches; I’m sure there are lots of good examples, but taking the path of least resistance I like to point at Star Wars as an easy example).
3. Trade organizations rise out of need. Aethora is a pretty rough world, and getting goods from one city to another is both extremely profitable and dangerous. This situation affords opportunities for players to partake in escort and delivery missions for various companies/agencies/organizations.
If I had time to do more detailed explanations of the cities and their governments, Aethorian economy, etc, id’d be in the wiki. At the moment I’ve got my hands full trying to keep the game fun and those extra parts get filled out when they are relevant to a particular mission or area description :)