I have known many people to fly with a bong. It's a perfectly legal item, and a pipe, hookah, or even cigarette paper should fall into the same category. If the standard is: you can smoke pot from it, then they should confiscate empty aluminum cans, aluminum foil, notebook paper, Bic pens, and just about anything else a creative and desperate high school student can come up with. What a security guard (even a federally employed one) imagines what you could do with your hookah should not be your concern, and they should not share their thoughts with you.

Pack the pieces in different bags, but I cannot understand why you should have any trouble.