That's because your PCs would rather go with splatbook spells that give Sonic spells the same damage level as other elements, despite the fact that few if any core monsters have resistance to it and it does normal damage to objects. If I had the choice of Shout, a sonic damage spell as it was originally intended, and Sonic Orb, a splatbook spell that ignores the greater power of Sonic damage, yeah, I'd definitely go with Sonic Orb.
That doesn't mean Shout sucks. It means that Sonic Orb is absurdly overpowered unless you rule that Demons and Devils get Sonic resistance, too.
Why, when all the other elemental-damage weapon effects are 1d6 elemental damage for a +1 cost, or 1d6 normal and 1d10 on a critical for +2 cost, does Thundering carry a +2 cost and only do 1d8 on a critical? Because it deafens, too, works better on objects, and because hardly anything is resistant to Sonic energy.
Don't base your logic on what YOU and YOUR players did when asked to choose between a Core spell and an overpowered Tome & Blood spell. That's like saying, "Yeah, I could have taken Fireball, a 3rd level spell that does 1d6/level, but why would I want that when compared to Heatsphere from this other d20 book? It's 3rd level, does 1d8/level, and does an additional 1d4/level the following round. Fireball is so totally underpowered!" No, Fireball was balanced. The other one wasn't.
-Tacky