I generally am not going to punish my guys for using Bioware/Cyberware outside of the RAW things, although I may add some complications (and occasional bonuses) for people sporting a ton of obvious stuff, especially cyber arms.
One of my guys "rented" a girl at one of the Yakuza parlors (I blanked on what they are called) and gave him some additional crap for his arms, basically having the person checking him in react to them and ensure he knew that no physical harm was to come to his "date," and any harm that was caused would cause additional charges to be made (or worse).
If someone is running around with a high end reflex boosters running active, I may have him do some twitching and stuff from time to time (especially if it is used).
