So lets make cloaks impervious to scanners, but use the Star Trek rules for cloaks and make it so that ships can't fire weapons while cloaked.
Okay, so this idea gave me pause, but I'm gonna go ahead and hit you with a "no" again.
First of all, I'd like to point out that weapons fire while cloaked
already puts cloaking on cooldown. As to it disabling shields, stealth ships are already a class of ships that have very limited capability in direct combat, and I think this would just be an unneeded nerf to their already-limited chances of survival once discovered.
Anyway, my primary issue with this idea is that it would basically nullify part of the usage of manually-operated scanners, just to justify logic-operated ones. When players are online, and aware that a stealth ship is in the area (thanks to the "Player has entered your space" notifications which faction players receive), they would no longer be able to actually scan this person out properly, leaving them at a disadvantage (no automated weapons can fire on a cloaked ship, as far as I am aware). This would mean that, besides a manually-operated defense (which is relatively hard to coordinate, against a rapidly-moving stealth ship), scouts would have almost no worries, even while contending with an actively defending player.
Without players involved, logic-operated scanners would still achieve very little in terms of base defense. As I've said in my previous post, most competently-built bases can defend themselves against a cloaked attack without issue,
with no need for any kind of automatic scanner. It is mainly just players that would be nerfed, and that is not desirable.
So, unless you want to dispute the idea that unattended bases, when built well, do not have a significant need for automated scanners, such systems only really hold water as some kind of small buff to defending players on a station (which manually-operated scanners do just fine right now, and better than they would with your proposal), or in fleet combat, as some kind of constantly-cycling early-warning system (also works just fine right now, with manually-operated scanners). I suppose they could also possibly be used in a large-scale grid to track ships across a large area, but this would require a way for their data to return home.
This last usage is the only one I am not opposed to. It would be interesting to see a different scanner block, which we'll call "Auto-Scanner" for the moment, which just cycles as fast as it can. Some kind of data-return mechanism would be needed; I think the simplest would be that it activates any adjacent Activation Modules or Buttons when it scans a player-controlled ship. I do not think this type of scanner should have the ability to put cloaking
or jamming on cooldown, though of course it would still notify any pilots that they had been scanned.