In Revolutions, we see Commander Lock tell the leaders of Zion that the walls will be breached in 12 hours. The very next scene (presumably running parallel to the Zion scene, or at least shortly after) shows Niobe leaving for Zion while Neo and Trinity head for the Machine City. Niobe’s ship doesn’t arrive at Zion until after the fighting has already taken place for some time. This means it takes many hours, possibly 13 or 14, to travel to Zion from all the various city sewer locations that are at “broadcast depth” to the Matrix. This implies that there is great distance from ship to ship if they are all scattered in unpredictable locations, which would be necessary to keep sentinels from finding them.
It is also very possible that human encryption methods are not good enough to prevent Machines from cracking the encryption and listening in on the conversation.
I actually don't have any theories about how the agents found out about the meeting, but I'm not sure if it's a detail the Wachowskis even felt the need to explain. Maybe someone noticed a very large group of black leather-dressed people going into an abandoned building and felt "shock" that alerted the system. Maybe someone tipped them off. Maybe the machines were able to trace the locations of their signals.
It is very possible that Smith found the location independently of the agents. As Smith approached the meeting location, Neo could sense Smith. So when Neo entered the Matrix, Smith might have sensed Neo.
If not, we know that Smith gains more power within the Matrix by taking over other programs. He inherits abilities of the programs he takes over, which is made abundantly obvious in the scene in M3 where he takes over the Oracle. We see Smith take over an agent when Smith fights Neo in the park in M2, so Smith inherits the ability to communicate with other Agents, the ability to be alerted whenever there is a "system alarm" (see Matrix System: Agents), etc. It is also possible that Smith is still connected to the agent system after he is destroyed and exiled in M1, and in that case, it wouldn’t matter whether Smith copied over another agent or not.
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