How about you can hear them tapping morse code on the ship hull?
Or one of them waves at you through a window?
Or you recognise the smell?
Or in the far distant future there are things called "scanners" that can see everything up to and including the type of underwear people are wearing?
Personally I try to ignore held pilots unless someone wants to get some RP out of it - like exchanges, or pretending there is someone who is actually known among them.
Try and play dumb around the information you do have. When people are willing to RP with me, when I'm playing Hans and his scanners detect any sort of "human cargo", I require that the captain of hailed ship to upload the manifest and the permit to transport passengers. Usually the people carrying slaves, lawful pilots and the sort tend to get nervous or refuse to RP the tight situation and just try and evade me. This gives me enough in RP reason to try and stop them.
At this point I usually play contacting the local bases and requesting a rescue ship in case push comes to shove (which usually do) and I have to recover 5000 cargo units worth of people in life pods/space suits. Well, it's hard, but it's fun. I usually get hurt a lot trying to type and pursuit and disrupt people trying to evade me.
Me letting smuggled human cargo pass depends on what the cargo is (I reckon slaves would be more difficult to identify than pilots from the local forces) and what the reaction of the smuggler is. Up until this point, unfortunately, nobody has demonstrated neither willingness nor creativity enough to have me purposely play dumb and let them pass. Probably because most people either will try and make a run for it, shoot me, won't play along with the whole thing or simply can't get around the situation in a satisfactory enough manner for me to let them keep moving.
Something I have always wanted to do as a smuggler is try to fly right pass a group of police/military with some lawful pilots in my hold saying: "Hold your fire! We have alliance prisoners onboard, kill us and you will be killing your comrades."