Seen ‘The Day the Earth Stood Still’ movie remake?
Then you know the power of nanites.
So how about nanite cannons? You can’t shoot them down with a gun like you can with fighters. They will eat your ships! (Just like radiation damage but without any friendly fire damage.)
After the ship is destroyed the nanites will continue to inhabit the wreckage in little cloud swarms. If an enemy ship passes nearby the nanites will go after it.
But if the ship that fired them is destroyed, the kill switch will activate like on the recent G.I Joe movie and the nanites will cease to function.
How about having the nanites with the ability to slowly destroy armour over time, yet have no armour penetration value themselves?