Glad you enjoyed the game so far.
Space patrol searches do detect illegal uncloaked cargo and confiscate it and fine you and you get a REP hit. As to Audra's response if you do illicit slave trading as long as your dealings are under the radar I think its consistent. That being said, there may be a bug somewhere (opened a CRQ).
The bot part I had to freeze a bit, as it was getting out of hand and players wanting all kind of stuff added that would have the game go off a tangent. Use of military bots for some purpose is still planned (currently only infiltrator mission...)