Besides the poor strategy is using throwing knives in home defense, we're actually talking about two completely separate areas of law here. The laws on knives are strictly about carry, and were designed to prevent "hoodlums" from going around armed in public ready to commit acts of violence. These laws have no effect whatsoever on the ownership and use of knives on private property.
When force is used by a homeowner to repel an illegal invader, it's all about the force and situational matters. The weapon used is judged strictly on it's appropriateness to the threat faced. Knives in general are classed as deadly force, and therefore should only be used against a deadly threat. If any legal action were to arise out of using throwing knives against a burglar, it be strictly based on if that was appropriate force, not because the weapon used incidentally is not legal for public carry.