I agree with Va1id's proposed nerf. I personally have never been able to actually obtain a Beacon Access Kit,

I have never even seen one in a shop,

so I never noticed any balance problems.

Though I can see how it would get spammed and how you could collect tons of scrap using it. It could potentially turn a regular game into Infinite Space if you hit enough empty beacons. Plus all of the other fleet delaying choices have penalties, minus drone parts/fuel/mines/etc...
Tying the chance of success to sector type sounds like a great idea. However, although it would make sense for the Access Kit to work better in civilian sectors and less in hostile sectors, the problem with spamming the augment mostly happens in civilian sectors due to the more frequent empty beacons. So perhaps it should just have a standard %25 chance of failure? With maybe a %50 of failure in nebula sectors since there are way more empty beacons there. It could have something to do with the fact that the beacons are maintained by a separate network, or that the Rebels have set up a firewall for all the beacons in this matrix already, or that the beacons are using a new frequency since they have only been built recently.
EDIT: Here's a couple more augment related things I noticed when I looked at the files again. It seems like there are no possibilities for enemies to use the new AE combat augs in the CE_ENEMY_COMBATAUG_RANDOM event. There are no Firewall Plating, or Mind Shield, or even Subspace Scanner possibilities.

A rare possibility of an enemy using two combat augments at once, with an Internal Generator, would not be bad either.
Also, for the "Your enemy is using dirty weapons!" event where the enemy uses a radiation projector against you, there is not choice for Adaptive Gel Suits. I thought you changed the name from Artificial Respirators to Adaptive Gel Suits so that they could be used to protect your crew in a wider variety of environmental hazards. This seems like one of those hazards.
Lastly, you could add some flavor text for the weapons and drone jammer failure events that say the enemy appear to be equipped with an "Advanced Targeting Computer" or "Improved Drone AI" respectively.
EDIT 2: One more thing, I don't really understand the need for the ASB Augment to use up 1 power. The missile cost is already a good enough penalty I think.
And is there any way to prevent the background from changing when using the ASB augment? If not that's fine...

I've learned to deal with broken stuff.
