Of course. Tobacco pipes are "tobacco pipes" ya dig. An old man smoking a pipe is no more legal than you bringing your "water tobacco pipe." On the other hand I would NOT bring it on a carry on. They might get mad about having that much glass on the plane, as it could potentially be broken and be used as a weapon (no clue if this is actually something they worry about but I wouldn't be surprised).
Im quite sure this wont be a problem, people travel all the time with fragile glass stuff, expensive vases etc. Someone on tc travelled with a carry on with 3 tubes and no problem, so the fact that its glass not necessarily a problem.
You want to risk your tube or your flight? You're just giving them a reason to take it. You may have heard of people doing it but they will check your carry on, ask you to put it in baggage and on the way send it to the sniffer. Too much risk for something that can be sent for $10 usually. Edit: cavity searches
Over course it'll be 100% clean. If iso/salt weren't effective at cleaning glass back to its original state, over time you'd expect to see residue building up, and that's not the case. At least not on any of my bongs.
Unfortunatly things can be smaller than you can see. Can you see that your glass bong is actually really hairy looking? no. Can you see the influenza? no but it still gets ppl sick. And older bongs do have a used look to them, specifically old downstems that are tinted a lil yellow.
if i cleaned my clear pipe im near positive i could put it in my luggage and bring it with me. its completely clear, and when i clean it with simple green, you couldnt tell it apart from a brand new one by smelling or with the naked eye. im not saying you couldnt get a microscope and see trace microscopic evidence, but theyre not going to do that, nor would a cop pulling you over. I dont see how it would be any different than if it was a brand new bong(which are legal)