At the beginning of the novel, Jim is aware of the war but not directly involved, and so he does not truly understand its terrible brutality. Ballard uses the technique of third-person limited narration, allowing the reader to experience new events just as Jim does, instead of informing about consequences and the disassociated stories of other people. Jim's detachment is partly because he does not understand the war, and later it becomes a coping mechanism to keep him sane; he cannot allow himself to fully embrace the horrors of war, so he keeps everything at a distance.

His mother's clothes were scattered across the unmade bed, and open suitcases lay on the floor. Someone had swept her hairbrushes and scent bottles from the dressing table... dozens of foot prints in the [spilled] powder, his mother's bare feet whirling within the clear images of heavy boots, like the patterns of complicated dances...
(Ballard, Empire of the Sun, Google Books)

This detached persona, coupled with a limited narrator, allows the reader to experience the horrors of war in the same order as Jim. Readers will know about many of the atrocities committed in the book, but seeing them through Jim's eyes allows increased empathy and new perspectives. Jim's personal changes are therefore partly a maturation process; he is not sure what to think, and so he tries to remain aloof, but he cannot help reacting in some ways, and the narration style reflects those reactions.

How does Jim discover the "realisation of war" in Empire of the Sun?

Certainly, the time Jim spends in prison camps and struggling for mere survival could be moments when Jim discovers the realizations brought on by armed conflict.  Yet, I would that the opening of the book, when the Japanese bomb the European naval forces in Shanghai and intern all the Europeans represent the first moments where Jim discovers "the realisation of war."  One of the major epiphanies that Jim undergoes is the transformation from his understanding of war as something that is a Romanticized vision of nostalgia from one that is forceful in its change and horrific in its consequences.  In an instant, Jim undergoes this transformation as he struggles to survive being separated from his parents and cut adrift in a world where there is little in way of structure and order.  This sense of forlornness and loss might be the first moments in the work, but also might serve as the first instances where Jim discovers "the realisation of war" in terms of what it is and not what Jim thought it to be.