One could make a case for the book's main theme being trauma. There are many traumatic events depicted in the life of the main character, Kikuji. While the other characters in the book are the victims of traumatic events, the trauma that harms Kikuji comes from his feelings for the people who have suffered or died.
When the novel begins, Kikuji has been orphaned by the deaths of his parents. Of course, this leaves him with a great deal of sadness, but it also leaves him feeling lost. This may be just as traumatic.
Kikuji isn't quite sure how to live his own life, and emulates his father by taking Mrs. Ota as a lover. This, and his father's affair with her, lead to her suicide. The trauma is compounded by Kikuji's troubled relationship with Mrs. Ota's daughter, who may or may not commit suicide at the end of the book.