We are talking about engineers, yes, but, guys like the research and development chiefs of Audi and Porsche, Ulrich Hackenberg and Wolfgang Hatz, or Hanno Jelden, head of the company's powertrain electronics.
These guys are top execs. Likely substantial performance incentive packages.
Such execs, like any CTO anywhere, could run a "special project" like this off the radar, to hit projected metrics, and bonus targets.
Don't take VW's word for it, here is the German prosecutor's take:
> The number of Volkswagen employees that orchestrated the diesel-emissions scandal that's rocked the automotive industry was likely fewer than 10, according to the public prosecutor's office in Braunschweig, Germany.
http://www.autoblog.com/2015/10/23/fewer-than-10-vw-engineer...
Often we engineers know things the CEO doesn't. I'm confident that happens across industries.