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.
Why not use a 12 guage shotgun pistol loaded with soft plastic pellets. A terrorist with half of his head blown off is "nutralized" real good. No damage would be sustained by the aircraft and no bystanders would be injured. But this is too simple to try, huh?