I agree with your first sentence but I don't think Na-Kyum is protecting anyone. Seungho favours him a lot and has made him his prisoner. Meanwhile, his teacher, who was also his only trusted "friend" (or so he thought) basically told him he was trash. What other choice does he have but to give in to the pleasure? Seungho would have had his way with him anyway. He admitted to himself that he liked the sex and since he can't escape it whatever he does, I think he did the right choice.
*made
You have a point and that could very well be the case. It's hard to say and we won't truly know until Byeonduck reveals NK's true thoughts.
NK is not in love with SH, nor does he have Stockholm Syndrome. Don't forget, SH threatened to hurt NK and In-hun if he ever left. Not to mention, the servant Kim himself asked NK not to wander off by himself because he and the other servants would get beaten up for it.
Because of his teacher's words and his love for him, I think NK now sees himself as a prostitute and he's staying because by doing it he'll keep his teacher safe and ensure that he'll get his government post. After all, SH is still sponsoring him. NK still loves his teacher despite how cruelly he was rejected. Remember how NK looked at the painting of In-hun right after SH slapped him? He decided it then and there. NK is selfless in his affections and this was even something SH commented on when he put that red dot on his forehead.
While I think NK truly does enjoy the pleasure he receives from SH, I also feel that NK would prefer to receive that pleasure from someone he loves instead.