Assuming there isn't any miracle scanning tech, we can extrapolate the process now except on an intergalactic scale. It would be incredibly ineffective. For intersteller trade to occur, then you cannot do any kind of indepth border control procedures at the jump nodes.
Modern border controls at busy ports are not very secured. Stowaways and contrabands regularly get across the border and pass by inspection. Now imagine if all the commercial traffic on Earth goes through a single port. The volume would simply be overwhelming.
Instead, I would suspect that border control takes place at secondary ports, the places that link the system with the associated planetary body, satellite, or space station, where the volume of traffic would be a lot less. This would leave room for smugglers/stowaways to hide in the space inbetween the jump node and ports, perhaps some hidden moon base or space station.