Even with the recent baggage belt construction overhaul, I feel that this question still remains un answered.
This is a snap shot of the baggage scanning area from the 2nd gameplay video.
At the end of the scanning process, we see a manual bag checking station (indicated by the red graphic showing staff requirement).
I guess the long run implementation of baggage scanning would tie into the Events feature.
Finding Forbidden items on a passenger bag would lead to detaining the passenger, interrogation, arrest, etc.
Letting a bag with Forbidden items through and on to the plane may result in trouble on board if passenger has weapons or crash if hazardous materials, etc.
However, my short term solution is as follows:
For every bag found with Forbidden items (for check in bag at manual station or carry on at security check), the bag is destroyed (deleted from the simulation), and you get a bonus (money added) for successfully finding said item.
If an item is missed and it is allowed on the plane, you get a penalty (money deducted) when the flight takes off, and if airline ratings is already implemented, then your airline rating drops a little.
This will result in a direct incentive for having better and more stringent security (more expensive, so you need something like bonus to offset the costs), where as if you run a cheaper security, the process may be faster, but may result in greater penalties over time.