Mods used to easily replicate this issue: Console Commands, LazyLib, and Practice Targets, none of which should be causing this issue. No other mods were enabled.
Scenario 1: A Drover, piloted by the player, mounting 1 Warthog wing and nothing else vs the Low Tech Practice Target; basically a shieldless Onslaught without any guns on it.
Without skills, a Warthog does 67 damage to armor with its initial volley of 3 Light Mortar shots.
With Strike Commander 3, a Warthog does 229 damage to armor with its initial volley of 3 Light Mortar shots. If you turn the music off, you can clearly hear the impact sound play way more than 3 times.
Scenario 2: A Drover, piloted by the player, mounting 1 Warthog wing and nothing else vs the High Tech Practice Target; basically a Paragon without any guns on it.
Without skills, a Warthog does 67 damage to shields with its initial volley of 3 Light Mortar shots.
With Strike Commander 3, a Warthog does 229 damage to shields with its initial volley of 3 Light Mortar shots. It's harder to tell if the multiple hit sounds are occurring as the shield impact sounds are less distinct, but I think that it is playing multiple hit sounds.
I cannot get this to replicate with Sparks or bombers, which I believe points to a projectile issue. Perhaps the projectiles are not despawning properly after the first hit, so they hit multiple times in a row?