Truthfully, if you are running mutiple ships equipped with missiles, only one of your ships needs Mag-Pulse Warheads. Have that ship fire first to proc off the effect and have the rest of your missile squad hit the target with concussion missiles for example.
For example, if points allow, my Kylo+3x missile Zeta SFs will be modified to have one copy Mag Pulse Warheads while the rest have concussions.