Why offload bags for missing passengers when flights are allowed to carry unaccompanied non-PAX air-cargo in holds?
Partial answer:

The rule about offloading passenger bags is known as Positive Passenger/Bag Matching. It was introduced after the Pan Am 103 bombing in 1988 where a bomb was placed in a suitcase that was checked through to New York without belonging to any passenger on the plane.

By the practices of the time, all bags tagged with the right flight number would be loaded onto the plane, without pausing to cross-reference them to passenger manifests. The investigation never found out for certain how the suitcase with the bomb had entered the baggage system (an inside job at Luqa airport was suspected but not proved), but the outcome was to require matching of all the bags to actual boarded passengers before departure.

So this is not necessarily a case where explosives were placed in the checked bag of a passenger who should have boarded but didn't -- but it is close enough to see that the risk is not pure fantasy.

The rule applies to all international passenger flights, but not to US domestic flights; the US authorities apparently have better trust in their ability to screen checked bags for explosives before loading them onto a plane.

I would assume that air cargo also undergoes similar screening and that is why it is not subject to PPBM rules -- even outside the US there is better time to screen cargo thoroughly than there is for bags that are only checked an hour or two before departure.



This Travel.SE question and its answers have more information about PPBM.