Getting it handed to me by the AI :(

[Alneyan]

You should put Supply Storages on your vessels, especially if you do not have enough shields to soak up the engine depleting attacks. Losing all your engines will destroy their supply storage, and you cannot fire anything (including PDC) if you do not have any supply storage, even with the Quantum Reactor (an unlimited zero still gives zero for the game).

Units may be another solution to take care of this matter, especially if they are lacking in weapons able to target units. A combined force of warships and fighters might do the trick if they reach the enemy ships nearly at the same time; you will take casualties, but hopefully your fodder should Last long enough to win the day.