but why is it unlikely for him to have not known, and also not been responsible for killing her?

The point is not what he knew then, but what he knows now. If he didn't kill Hermione, someone else did. Whatever would motivate someone to kill Hermione is very likely to motivate them to frame her and get her sent to Azkaban, and require the same ability to evade the Hogwarts wards. So if Lucius did not kill Hermione, this is strong evidence that she was framed. Contrapositively, if Lucius still denies that Hermione was framed, that is a tacit admission that he probably killed her.