The AI is a highly accomplished builder of Thieves Guilds. I doubt that even if I made it a priority I could put a thieves guild in every single city in my empire.
Yeah, it's almost annoying. I usually have to destroy over 20 thieves houses for campaign...

Anyway, as you said well, the AI is not that bad in using agents and finding ungarrison cities or castles. He is also tough in the in the religion warfare and also, well, you can't complain with lack of enemies. You can be at war with over 10 powerful nations, even the whole world if you wanted. The only 2 main problems are the resources management, which is hardly a problem when the AI seems to take resources, money and troops out of pure air, and the battles. They should have taugh the AI that a frontal charge isn't the only way to fight an enemy, that chasing missile cavalry with infantry is suicide or that cavalry units running for their armies' rear are not intend to leave the battlefield...