Interesting.. but that still sounds like a bug... Changing/fixing that behavior.. now that would be something.
It's not so much a bug as an oversight. They probably check if it's one of the two shuriken items and tell it to use the alternate animation if it is, which is the regular shuriken's animation. Keep in mind one guy probably set up all these animations and another coded the actual throw command, the one who did the command may not have even been aware they were supposed to use a different palette. The same is true for the dancing dagger, when "thrown" by using it as an item it uses the green and gray palette used by mythril weaponry, rather than the gold palette the knife actually uses. That is slightly different, that animation doesn't pull the palette from the weapon data at all, I don't know where it gets the palette since it isn't a part of the spell either.

Heh, I thought of something right after posting this. Remember the unused "dancing sword" animation I posted about a while back? It grabs the palette from there. Proof that the original dancing dagger was just going to be a normal attack animation?
I might as well point this out, but I tried throwing that crappy junk item (I forget what it was called, but it was the item given to you for failing the entire trial in Cecil's trial) and I don't recall it playing the normal sound effect, even though it used the shuriken graphic (for whatever the reason). Other than it doing 1 damage (0 attack power), that was the only notable thing.
Yeah, but that's FF4 Advance, that's entirely different. In the original sound effects are directly tied to the animations, if it's playing a different sound effect they must have changed that, anything using the shuriken animation in the SNES version will sound like a shuriken being thrown.