No, what these guys are reporting as "unprotected" transports is in fact, what happens when the AI make a transports, loads it up, and fly it to the waypoint. The AI is programmed to do this to fleet ships together. Only when they actually arrive at the waypoint and fleet with their escorts do they become guarded. So, of course, when it's still fleeting, it will be unprotected. If you're running around in their backyard causing all kinds of havoc with fast ships, that's just a strategy that the AI simply cannot counter due to its innate lack of "space security".
The problem isn't that the AI isn't guarding it's transports, it's that it's not guarding it's space well enough. Most players will be able to outsmart the AI with faster ships doing hit-and-run tactics while avoiding their major fleets. If it was me, I would have kept some ships in orbit of my transport producing planets and border worlds to act as an "interceptor". It will probably be a medium with an emphasis on engines that is designed to launch out and strike down any nearby enemy ships that it has a good chance of winning against. This would include your havoc cargo ships, transports, traders, or scouts.
Another balancing feature would be to change how sensors work. First, heavily nerf Eyes of the Universe (or change how it works, maybe an espionage bonus instead), because a player will rush for this as soon as they are able, and then it's good night because it gives the player such a massive strategical advantage. Second, make each sensor tech give a sensor bonus, then apply that sensor bonus to planets as well (or make ships in orbit retain their sensor range). Then increase the AI's research priority on the first 3 sensor techs (really cheap). This way, the AI will get a lot better at detection and will behave much better to sneak tactics.
IMO, if it will take too long to make the AI play the game better, then you should tweak the game in order for the AI to play better.
