I haven't noticed any correlation between higher payouts and secretive passengers myself, it seems pretty random to me. In any case, I don't mind taking secretive passengers as I've never had one quit on me after one scan. I came close earlier today - I submitted to an interdiction in order to fight, and when the NPC scanned me the passenger's mood went down to 'miserable' which I assume is the lowest level before they sack you. At the destination I dropped a heatsink, engaged silent running and went full throttle through the slot to avoid another scan. So even in this scenario you can still get paid. Mostly they'll just go down to 'happy' or 'content' after one scan though.
EDIT: By the way, secretive is different from criminal. The criminals have 'passenger may be wanted in multiple systems' in the description and do tend to pay higher. Fair enough, as you will get destroyed if you get scanned on the way into a station with one of these. The secretive passengers don't want to get scanned for reasons of their own - maybe crime related, maybe other reasons.