SPOILERS AHEAD - Don't proceed if you haven't seen the movie.
I don't think they give any definitive answer as to what Miss Emily had concluded regarding souls in the clones. However, it makes sense that clones created from human DNA would as others have mentioned be effectively a twin "copy" of that original person. So if anyone has a soul, so would they. We know they were genetically modified so that they were sterile, as they did not want to worry about pregnancies in the clones and knew that as Tommy says, the urge to have sex is a natural part of the human experience. The reason why many things don't make sense to them, such as the comedy on TV shows and why it's odd to be peering into the travel agency is they were only taught what the school thought it would be beneficial and/or necessary for them to know. We also get told indirectly that Hailsham students have grown up much more sheltered than others in regards to the outside world.
I did get the impression that Miss Emily likely refused treatment obtained from clones due to her personal convictions and would live out her natural lifespan. No proof other than her beliefs about how clones should be used in society, knowing they always would be, that she could not change it, so likely may not have wanted one to die for her to live longer.
I also believe it is very important about Kathy and Tommy's visit with her. She tells them that they were trying to prove to the public that clones were basically human, trying to determine (and hopefully prove to the public) that clones had souls and it was wrong to be farming them like cattle. However, now that people were being cured of lung and breast cancer and Neuro diseases? That they would never give that up, it was just much easier to hide the clones from the public, literally treat them like a commodity and look the other way. Basically, the battle was lost.
I just wanted to weigh in on one other thing. These children are told from birth they are special, they spend 18 years hiding them from the world and indoctrinating them to the idea that they were born to give their lives to save the lives of others. It's not like they lived somewhere else, knew another life, and then were taken at age 8, 10, or 12 and then told they no longer had a future. I am not surprised at all that they accept their fate. Their whole life is being scanned in, scanned out told what to do, any aggression or other bad behavior is managed early. They are trained to believe this is their altruistic role that society has chosen for them, that's why they were "born", and they have a predetermined path that each of them will follow.
To each their own...opinion
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