But why does the writer refer the things(malnutrition, exhaustion and disease, suicidal despair) as citadels?
He doesn't. "these citadels' refers to a noun in a preceding sentence, something like:
".......Malaya.............for the prisoners of war interned in Japanese Concentration Camps. Piled on top of malnutrition, exhaustion and disease, suicidal despair was the big killer in these citadels of degradation."
Student or Learner