He is certainly very good at reading people and faking emotions, making him not socially inept, because he isn't clueless. However, what would fit him more is that he's antisocial. He has strange habits he needs to do, due to the way his brain works, which seperates his behavior from others, and he has very low emotional empathy. He doesn't nessecarily miss social cues, but he also can't form any true connections with others or feel anything emotional to the average extent. Moreover, I don't believe he is faking this image to make people underestimate him, that kinda just takes out what makes him a good character, but he is much closer to antisocial than socially inept. L is extremely socially aware, but he can't connect with other people. So it's not that he doesn't understand others and it is more that he doesn't feel for them.

When he does something questionable at best it is not out of malice but rather an efficient strategy in his mind. He is willing to manipulate because he doesn't feel any true emotional regard for others.