The AI in the missions use the cloaking device from time to time, but I often see a ship cloak and still get hit by weapons fire and explode right afterwards. Doesn’t seem to be much protective effect (the cloaked ship stops firing as described though). I have seen cloaked ships sneak away successfully though, so maybe it’s just all the shots already en route/being fired at the beginning of the cloak hitting. Maybe ships need to be smarter about using the cloak, engaging it earlier so they actually survive the cloaking… They also tend to engage the cloak when there’s no enemies around.
I’ve noticed shields repair when partially depleted, and shields disrupted and come back. I just noticed one of my cruisers survive a mauling with its repair units intact, and be able to repair all systems (including all the shield generators) and hull. However, the shields never came back online - are shields gone for good once they’ve been downed?