It suggests that while the outer appearance has changed minimally, there is no life inside.
A shell is a hard outer cover, and it may survive the death of the creature that lives inside it. This can be literal.
This is the shell of a crab that a caught and ate last week.
or apply to a city to mean that the buildings still stand, but the people have either fled or are in hiding.
Or it can refer to a metaphorical loss of life:
After his wife left, John became the shell of the man he used to be. He rarely left the house and just wandered round the house in his dressing gown.
So while Khartoum has not been "reduced to rubble", there is little sign of people living in the city.