Just before you fight the third boss, Zhao uses something on you. If you have the upgraded biochip, you essentially have a permanent EMP. Your HUD is messed up, so you don't have a radar, health/battery meter, ammo, etc. I found I was able to use augmentations though (such as looking through walls). I just didn't know how much battery power I had left.
Best Answer
According to the stealth tutorial video, a lethal takedown makes more noise than a non-lethal one.
Neutralizing an enemy without killing will award you a +20 XP bonus ("Merciful Soul").
Knocked-out hostiles can be woken by other people who happen to find them. Obviously, this can't happen if they're dead.
I'm not aware of any impact on the story, though there is a Steam achievement (Pacifist) for not killing anyone except bosses.