We know that Lucius has seen Harry several times and that he knows he is most of the times with Hermione and Ron.
I'm re-watching Harry Potter and in the movie, Hermione disfigures Harry but not enough and the Snatchers are not sure if he is himself and from what I remember from the book, the Snatchers identified Hermione who was known to be with Harry and therefore brought them to the Malfoy Manor. In any case they believe it could be Harry, why wasn't Lucius sure if he was Harry? Maybe Draco didn't want to identify Harry for any reason but I'm sure that Lucius would have.