While I'm not sure about cloaking the mobile AI eyes, I do like the thought of roaming defense systems like that.
Could force deep strikes to have to be more surgical in nature rather than going in with a large force sledgehammer style.
Stuff like that could at the same time keep minor factions like the Dyson from wreaking too much havoc deep in enemy territory a half-dozen hours before you ever encounter them.
Though I'm not sure if this may force players to have to spend too much time getting intel on a wide spread of planets around the one you want to strike, or alternatively take attention away from your strikegroup since you have to keep your eyes on surrounding systems in case the AI is closing in on you.
Maybe add a sort of warning that notifies you about this sort of defense becoming active against you as long as you have the systems it moves through scouted. So you have some time to react a good bit before totalhelldeath breaks loose around your fleet, without having to stay on the edge of your seat the entire time, which could get annoying.
Also, I like the thought of the AI getting the ability of sending waves into their own systems if they deem it necessary. They have those warpgates all over the place, why shouldn't they use them for defensive purposes, too? Waves aimed into deep AI territory may have shorter countdowns, too.