I'm trying to maximize XP earning, and I know there are some missions that at least one of these bonuses are not available. So on which missions can I actually earn these bonuses? Or to put it in another way, how many times is it possible to earn one, or both of these bonuses?
Credit to Darth Bieber on Trueachievement.com. (Gh) = Ghost, (SO) = Smooth Operator.
Sarif Manufacturing Plant (Milwaukee junction):
Tai Yong Medical
I don't think anyone has a specific list, but to speculate:
On a side note, I wouldn't worry too much about maximizing XP. Almost nobody has a playstyle that varies so much that all of the augmentations become useful.