The AI will only do what it is programmed to do. The AI would not be programmed to flood you with cloaked ships, only use them for scouting and raiding purposes. What you as a player use it for is up to you.
Sorry but I have to strongly disagree with this. This is not a case of "using size one missile salvo to overwhelm PD because I'm abusing the fire control mechanics". THAT is an exploit and the AI should not do it.
If what you propose is implemented the way you wrote, that using "cloacks" is the best TACTICAL and STRATEGICAL solution, then the AI should definitely do it, else it's just a very dumb AI. It is not a mechanical exploit, it's simply doing the best tactical and strategical choice.
A cloacking system does not breaks balance either if it is very ineffective, or extremely costly. Of the two, I'd prefer the extremely costly way, because that does not imply dice rolls that I may win or lose just because of luck. A costly cloacking system means my successes or failures would be the results of my planning, not blind luck.
If cloacking is cheap and effective then it's just completely out-of-wack balance wise
If it is relatively cheap, then as I wrote before I can and should build (and the AI should too!) lots of kamikaze cheap ships and flood the enemy territory with them, because they cannot prevent me from doing that!
I don't even need to do that. I can simply make cloacked ships which are faster than the enemy. They don't even need to be that cheap. Just make them faster, and flood the enemy systems with them. Once I'm through a blockade, how is the enemy going to stop me? Jump point defense is the only real defense against an enemy decently faster than me. If that becomes meaningless the only solution is to defend a few key locations with orbital defense bases. How long before that becomes untenable? How long before I control your systems, and you're relegated to staying close to your planets?
Sure, they will eventually all be hunted down, but so what? If they deal more damage than their cost, it is well worth the effort! Plus I disrupt the enemy and probably force him to mobilize his fleets, which makes him weaker in a lot of places.
A cheap and effective cloaking system completely breaks any semblance of balance. In fact, its' not asymmetrical warfare at all, it becomes the new normal. It becomes the default solution that every ship should mount, because it can be useful in so many ways both offensively and defensively that building a ship without such cloaking system is suboptimal. Not to mention the extreme tedium involved in the result of having a bazillion one-ship task forces in every system, trying to harass OR prevent harassment from the enemy
And once again, it has nothing to do with roleplay. That is that, this is this. Have you looked at the attrition rate of airplanes, tanks and infantry in either of the world wars? How many suicide or bordeline suicide operations were conducted? How many lives and equipment thrown in the meatgrinder? And even more so in an space war against aliens which may eat you or turn you into fertilizer?
In a struggle-for-survival war EVERYTHING is completely expendable. You are afforded the luxury of being concerned about losses only if you are so superior compared to your enemy that you're going to win anyway. Or if the consequences of losing are small. The best way to fight in a serious war is always the most cost effective one, and so if kamikaze ships are the best possible solution, you can bet they will be used.