Of course, it would be silly to assume that just because the torpedos look identical means they are. Every other aspect of technology seen in the franchise evolves; why would torps be unique in this regard?
Perhaps there was an evolution in technology such that during the time of the Kelvin shooting down torpedos was (considered) a viable approach, while by Kirk's time that was no longer considered the case, to the point where usually they didn't even bother trying.
Perhaps there was an evolution in technology such that during the time of the Kelvin shooting down torpedos was (considered) a viable approach, while by Kirk's time that was no longer considered the case, to the point where usually they didn't even bother trying.