How can they sit for secular studies but not for religious studies? Ela Mai, they're not interested. So like @ExGingi said that is something to be worked on. Although I think he was saying it's due to the teachers. I agree but I think it has much more to do with the students priorities.
Secular studies, generally speaking, are setup into multiple subject, none of them more than 45 minutes long. So you're learning something different every hour. In limudei kodesh, that same idea can be facilitated by breaking up the day with Halacha, Mussar, Tanach and not focusing so long on Gemara.
It's also not just about the material, but also time of day. When we had 'English' back in the day, we knew that we only had 2 hours left to the school day, we also had it after lunch, so most of us weren't hungry (I remember how 'focused' I was at 11:45 in the 3rd hour of Gemara). Some kids learn better in the morning, some better in the afternoon. Some kids take ADHD medication, which makes them able to better focus in the morning, and less in the afternoon when it wears off. Some kids are sleepy and ultimately wake up. In modern yeshivas, where the day is divided more or less equally, they alternate weeks between Kodesh and chol so that each kid gets them at different times of the day, and it breaks up the monotony of the schedule. (i.e. If there are 2 classes in the grade, Class 1 has English first Week A and Kodesh first in Week B, class 2 gets the opposite).