I wonder if it isn't easier to buy a laptop with two drives. Install a regular OS on the first, hide the second in the BIOS and nobody will notice.
The people doing the cloning / data theft would have to know about your particular model. Obviously, you encrypt the second drive, that in itself contains a hidden partition in case they do discover it.
The project here is quite neat. But I wonder if your idea would also work and ask myself how competent the forensic teams of airport security really are. Or even if they are, they certainly don't have a lot of time per device.
IT specialists are expensive and it would be shame if we waste that on something benign as airport security which was mainly established by paranoia and the wish to save face.
An what exactly are they targeting? Are they looking for howToBlowUpAnAirplane.txt? Just some industrial espionage? Just some display of authority? I don't really get what would prompt these measures.
Was there ever anything they found on a device someone took on a plane?
If you're only trying to slip by a cursory inspection, mount the second drive in your computer but don't attach any cables to it. Could be trickier depending on how drives are mounted in your laptop.
The people doing the cloning / data theft would have to know about your particular model. Obviously, you encrypt the second drive, that in itself contains a hidden partition in case they do discover it.