I do think that the hagwon system and the crazy work hours the parents endure contribute hugely to the problems Korea's seeing today. Students are given incredible amounts of "freedom" from a very young age, well before they are mature enough to actually deal with what is expected of them.
Take a hypothetical boy, "Minho." He is the oldest son in his family, and his parents expect great things of him. Accordingly, they try to give him all of the advantages possible to help him get ahead. Minho goes from school to hagwon to hagwon to hagwon is often expected to get from place to place under his own steam. This creates in him the understanding that he is supposed to be out roaming the streets at all hours -- that's how his life works. Through his schedule, Minho is being shown that he is an independent entity who can and should be in immediate control of his own daily schedule.
Minho also exists in an environment with little to no disciplinary continuity. As many of us know, the enforced "rules" of most hagwons basically amount to "avoid complaints at all cost." Unless he's being so bad that he's actually driving away other customers, his behaviour falls within acceptable limits for most institutions he will attend. He also knows that, no matter how terrible he was at math academy, there's no way his math teacher will call up his science academy to let them know that. So even terrible misbehaviour usually only has consequences for a few hours, maximum. The odds of Mom and Dad being involved in any disciplinary issues that may have arisen over the day are slim -- to tell the parents something like that is to make them lose face (to be avoided at all costs!), and risk losing their money in return.
Fast-forward a bit. Minho is 16, has been operating basically on his own for years now, and is getting pretty tired of the grind. Today he skips his hagwon classes, takes the money that was supposed to buy him supper, and spends his afternoon and evening in a PC room. If Mom and Dad do find out, what recourse do they have to put him back on the straight and narrow? Personally escort him from class to class? Even if they had time (they don't), everyone else would notice, and they would lose face in front of the hagwon staff and the other parents. Stop giving him money for supper? He'll starve; you're a terrible parent. Don't send him to hagwons, but instead study with him at home? Deprive a student of extra, specialized learning time!?! Are you insane?!? "Terrible" parent.
Minho here isn't even doing anything too terrible. He's just skipping out on some classes and wasting his parents' money. But the system isn't set up to allow anyone to curb his behaviour without going against some of the strongest forces in Korean society -- the need to fit in with the group, and to save face as much as possible. And Minho, used to being in charge of himself without strong, consistent adult oversight; Minho, taught by his school and hagwons that he, as the educational customer, should be given whatever he wants -- Minho, he's a perfectly bright kid. He knows he can't escape the system that's grinding him down day after day. But he can work that system, pitting the pieces against each other, pushing the boundaries where he knows there's give. And who's left with the power to straighten him out? Eventually, the army. That's about it.
Teenagers are designed for rebellion. The current educational system in Korea (or at least Seoul and Gyeonggi) just seems to be setting them up to do so in impressively effective and (often self-)destructive ways.