Why is "The Souls" a good name for these students?

In the novel, "The Souls" refers to Nadia, Julian, Noah, and Ethan. "The Souls" is presumably a good name for the students because it highlights the transformative journey each of them has taken.
You can find the answer to your question in Chapters 8 and 11. In Chapter 8, Mr. Singh confronts Mrs. Olinski. He makes a mysterious proclamation: he knows she almost chose Hamilton Knapp to be the fourth member of the Epiphany Academic Bowl team. Then, he proceeds to surprise her even further by saying that Hamilton Knapp would have been a "disastrous" choice. 
Mrs. Olinski becomes defensive, mostly because she feels unsettled by Mr. Singh's uncanny revelation. However, Mr. Singh makes another mysterious proclamation:

"Think of the atom, Mrs Olinski. There are energies within that tiny realm that are invisible but produce visible results . . ."

According to Hinduism, each soul goes through a cycle of life, death, and rebirth before it obtains moksha, or liberation from the earthly existence and all its accompanying challenges. Every soul that is reborn into a new body often keeps its previous experiences and acquired wisdom intact.
In Chapter 11, Mr. Singh tells Mrs. Olinski that the children have all gone on important journeys. Each has made a significant discovery on their journeys: that there is kindness in others and that this same kindness can be found in them as well.
So, The Souls is a good name for the students because it perfectly reinforces the journeys they have taken and the important life lessons they have learned along the way. The students' journeys mimic the soul's journey through the cycles of life, death, and rebirth.