If I have a bunch of cloaked ships in an enemy system, do his planets take the happiness hit automatically, or only if they have sensors in that system capable of detecting the cloakers ?
No, cloaked ships should not affect happiness levels. When I once noticed that they did a long time ago, I reported it to MM and he fixed it. If you notice anything that seems to show cloaked ships affecting happiness levels you should report it to MM also.