It doesn't sound (pun intended) too far-fetched. I used to dabble quite a bit with air horns and whistles (railroad, marine and industrial), and testing some of them would produce nausea - not mild nausea, either - for about fifteen minutes unless I used both plugs and earmuffs... even that didn't always work.
Ed
Assume this gimmick does work. Assume also that the hearing damage to the other passengers isn't permanent. (I don't give a damn if it makes the hijacker puke his guts out and renders him a babbling imbicle who'd make Barbara Boxer or Pat Murray look intelligent). The major problem is how a temporarily deaf pilot is going to communicate with the control tower to set the plane down safely. That is a far bigger risk than having a soft hollow-point .38 penetrate a window or the fuselage.
Guns can be aimed with far more precision than sound waves. Even the anti-gun crowd should be able to figure that out.