I had a three scene tour. The first scene had a sound hotspot, with a rotational effect. I deleted this using panotour interface, but the sound wouldn't disappear. I rebuilt the tour in a new directory and the sound still didn't disappear.
In the end I edited the .kpt file to remove the sound hotspot, and then the sound finally went away.
Meanwhile, the only way to remove sound spots is the way you did : - Edit the project kpt file with a text editor - Find the "Spot" nodes with "SoundSpot" attribute set to true - Find the one you want to deleteamong those sound spot - Delete the 4 lines describing this spot, beginning with <Spot> and ending with </Spot>