Phased Munitions are useful against sniper fleets that have regenerating shields. Even if you could not fully deplete their shields, you could still deal direct health damage and eventually destroy them.
Phased Munitions are nowhere as useful as Iridium Arrays, which dramatically improve the accuracy of your weapons. Even if you can ignore a portion of enemy shields, your weapons are still useless unless you can hit the target in the first place.
Phased Munitions are most commonly equipped on The Bridge along with Iridium Arrays to guarantee damage against snipers.