I managed to one-shoot one of those mothership with my FAC squadron. 20 FAC Hermes, each with 8 box-launchers firing MIRV separating in 4 heads dealing 4 damage each.
Meanwhile, in my home system, 30 cruise missile from planetary fortress, firing from 1.5 billion km away, dealing 50 damage each, didn't manage to one-shoot it. But the second salvo did.
Of course, the real problem is the shield. If you don't have a strike strong enough to pass the shield, you will never destroy it.