If I am to believe Braga, which I do, Enterprise apparently existed in a separate timeline created after events set in motion by the arrival of the Enterprise-E
The Iotians are highly intelligent and were able to connect the dots. Horizon
didn't have transporters. Kirk stated to Bela that he would explain the concept of the transporter after he beamed down. Events on the planet's surface put a kibosh to that. However, they saw people beam down, they knew there was a ship up there, and they knew that the Fed might want to negotiate with the bosses to get their people back. I think their level of understanding would be about the same as ours, if placed in a similar situation. And, remember, these are the same people who described phasers as "heaters".
had an atomic matter pile. This was the old name for a type of nuclear reactor. An example of this reactor was the Chicago Pile-1. [http://en.wikipedia.org/wiki/Chicago_Pile-1]