Is it considered a lie to say, "If I had known it was you in the car, I would have honked at you," when I knew it was her car but was unsure who was inside, and I did not want her to know? And what should I do in both cases?

Offering greetings and spreading peace are among the great Sunnahs of Islam. Honking a car horn or signaling with the hand while offering a greeting is considered spreading peace. If you know that your friend is in the car and you signal to her while offering greetings, then you have spread peace and fulfilled the Sunnah (definition). However, if you did not know who was in the car and refrained from greeting her out of fear that it might be her brother, then this is not a lie. But if you knew of her presence and said that as an excuse for not greeting, then this is a lie, and you must repent and seek forgiveness.