He might think that Harrymort is toying with his son for pure amusement, Bellatrix-style; or that Dumbledore set Hermione on Draco.

But he can punish Hermione as a demonstration of his ferocity now, while he waits and hopes to find the real villain later.

Lucius probably knows that he doesn't know enough; on that he agrees with Harry. The difference is that he doesn't see that as a reason to let Hermione off; he sees Hermione as at least an opportunity to send a message to his real enemy, whoemever he is, not to take the House of Malfoy lightly.