Gaming is for having fun. Fun requires clear rules.
Hint: read the examples in rulebook
On page 17 it's clearly shown that one player hits with 5 missiles.
3 are assigned to a player without PD and 2 to his ally with PD.
The player with PD hits missiles with one antimatter. Ha also has a splitter, which allows him to destroy 4 missiles, but he only destroys 2 assigned to him.
Point Defense: After your opponent has rolled and allocated the dice for Missiles of one Ship type, you get to fire all your Cannons once against the incoming Missiles before they hit your fleet. Each die that hits destroys a Missile. Your Computers affect the Point Defense, but your opponent's Shields do not.
Note that tech description mentions your fleet. Combined battle rules only make both allies fighting together in a battle, but still each operates his own fleet separately in this battle.