But they did install really badass launchers in the docking pylons. Giant, almost starship-sized boxes with the apparent sole function of spitting out torpedoes from a single orifice.
The end effect was a nice "layered defense"... The only thing I regret is the disappearance of the original torpedo launchers. Unless we are to interpret the "Emissary" VFX as showing the torpedoes coming from the middle of those weapon sail phaser/torp combo things? But that would take some doing.