yes, you read 中 as ちゅう , and 中３ as ちゅうさん
中３ is a shorthand way of writing 中学校3年生 which is (Japanese) Junior High School 3rd graders or in other words, 9th graders.
so 中３の２５％ would be "25% of (Japanese) 9th graders"
so the full translation of
"Twenty-five percent of 9th graders have difficulty understanding short passages."
Thanks to @Mars and @Eiríkr Útlendi for suggesting the more accurate word choices.
After all this editing, I realized one final point that can be made: in the expression 短文も理解困難, も carries the meaning "even", so the most apt translation would be:
"Twenty-five percent of 9th graders have difficulty understanding even short passages."