I have a question about the bonuses given to raiding and hacking from the protean armories and cipher bots. Does the extra bonus % improve your chance to steal or does it improve the quantity you steal?

Chance to steal.

nope, it is purely based on amount which is a variable in itself.

look at it this way if you could steal a max of 100 points of X, then the protien would give you a max of 108 points of X

Are you certain? I've seen the effect my proteans have on my base raid chances.

They increase the chance to raid/hack. Nothing more. The amount you steal is a separate calculation based primarily on rank differential.

Do believe the size of the pool you are raiding/having from is a factor.

couldnt say ive had them for longer than ive been raiding bases, but im pretty sure it goes off of how much you can take. especially considering that a +% success rate is a rather arbitrary and wasted boost. I can tell you though that it seems that I take more witht he Ciphers on than if they are off, never uninstalled the protiens, but then again I dont raid that much so I never really had a reason to.