The funny thing about Stockholm Syndrom is, it can happen even IF you are fully aware of what it is and how and why it usually occurs. It's a survival mechanism after all, so the brain doesn't care, whether you know if and what's happening as long as it helps keeping you alive.
At this point, Heewoon can simply fight it (and Kangwoo) and literally die (we all know, Kangwoo is simply going to actually kill him if he tries to snitch or leave him.) or try to make the best out of a fucked up situation. One of these options is better than the other for most people at the end of the day.
As long as options two is somewhat bearable and as long as he listens, acts cute and does what Kangwoo wants from him, he is living a relatively nice life. It could be so much worse for him and he knows it.
It's not ideal, it's definitely toxic, but at least he's alive and can fool himself into thinking, he as a loving and caring boyfriend most of the time. For a lot of people that is enough, especially if the other option is literal death or living in poverty and misery and being hounded down by loan sharks your entire life. But Heewoon doesn't even really have that option anymore because, again, Kangwoo would simply kill him or make his imprisonment a hell of a lot worse than it currently is, so at this point Heewoon simply doesn't have the power to change anything unless he actually wants to die.
I know it smells like Stockholm Syndrome, but the MC has conscious of his situation and decided to accept it somehow.
The ML obsession is totally unknown to me, but then again, I don't care. Obsessed ML never makes sense anyway.
Hope there's a happy ending at least ╮(￣▽￣)╭