In my most recent game, the AI players declared war on me several times. The presence of my ships in their zone was apparently enough to trigger this. I think that the AI declares war too easily especially when it can't back it up. If you don't have weapons, you wait until you do to declare war, there is no strategic advantage to declaring war early. If you don't have weapons, you don't demand tribute from much more powerful civilizations either. You can ask politely and if they refuse, you don't make threats. An AI who has no armed ships and money can bribe a civilization who does have ships to attack my civilization or it can purchase ships from armed civilizations before declaring war. The move that would make sense would be to send ships reasonably close to where they can attack something before declaring war.
In one case I had my armed survey vessels (2 of them, one purchased from the Altarians) in a fleet to explore anomalies. This one AI (Altarians) declared war on me despite the fact that my destination were anomalies not that civilization's shipyard or starbases. They had no armed ships at this point. The result of this declaration of war was that they lost their single shipyard and starbase. One move later, they asked for peace.
In one case, I purchased armed ships from the Iridium corporation, and as those ships were heading out of his ZOC to go to another territory where my ships were fighting another civ, the Iridium declared war on me. Now they sold me those ships, so those ships should be given a number of moves to get out of that civ's ZOC.
In the 1500 - 1700's it was not uncommon for sailing vessels to be armed because of the presence of pirates in both International waters and waters in the ZOC of ships. The presence of armed ships was not considered an attack unless an armada were to show up. An armed ship was not considered hostile unless it opened its gun ports, the equivalent of which in this game could be to detect a weapon's power up.
If a traveling merchant took defended itself from a pirate and captured him while in another country's ZOC, that merchant was usually rewarded by the governor of that colony or government representative. That merchant taking down the pirate was not considered a force hostile to the country whose waters the battle took place.