The books Holden read did influence his intellectual development, that is why it is so sad that he keeps failing out of one school after another because he is so capable. It is not his intellect that is holding him back, it is his emotional trauma and unresolved crisis that keep Holden locked in isolation and unable to participate in school.
Holden does well in only one subject at Pencey, English. He tell us that he is familiar with the curriculum in English because it is the same as his former school.
"I passed English and all right. I said because I had all that Beowulf and Lord Randal My Son stuff when I was at the Whooten School." (Salinger)
Holden spends a lot of time reading. For example, he has taken a book out of the library, and he got the wrong book, but he read the book anyway.
"They gave me Out of Africa by Isak Dinesen. I thought it was going to stink, but it didn't. I read a lot of classical books, like The Return of the Native and all and I like them and I read a lot of war books and mysteries and all, but they don't knock me out too much." (Salinger)
As a reader, Holden developed his intellect and was capable of getting really good grades. The more you read, the greater your comprehension, not only in subjects in school, but in understanding the world. It is possible that Holden was too smart for his age, too philosophically aware of what life was really about for a boy of 16.
When other kids his age are acting carefree and not paying attention to important subjects like death, Holden is trapped in unresolved grief trying to understand the death of his little brother within the larger question of what is life about anyway?