Iirc, cybernetics got basically nuked; its replacement came from th'talents, your pragmatic score and ego stat, and however th'blazes cybernetic dysfunction chance got moved around. Near as I can remember (and it's totally likely I'm forgetting quite a bit) there's no longer any skill that effects dysfunction chance directly. It was a bit back, yeah. Somewhere on the forum, I think someone had the formula being used by the code posted (or at least named whatever file in the source is detailing it), though th'blazes if I can remember where.
As for th'when, I think it was around th'time that Mistah H. did that whole (fairly) radical revision of th'skill/talent system; not, as you said, terribly long ago. Most (not all, of course) of GH2's systems were basically identical to GH1, earlier on. Th'documentation just hasn't really been updated yet, s'far as I c'n remember. Though yeah, th'documentation in-game is still from pre-skill revision, mostly. There's quite a bit wrong with it, I think, for all that it's still 'mostly' accurate.
For what it's worth, asking about how much things are going to cost/pay is supposed to affect pragmatism... somehow. It's a lot easier to get pragmatism to go away than to keep it; but generally, being a jerk without going to the point of triggering intimidation skill checks seems to be th'path to bringing it up. Or edit the savefile, whatever (Protip: This is a lot faster, especially if your character gets hit with a high starting mysticism score.).