While your ship is busy blowing up the empty ships, it's not somewhere else. Another one of their planets might be cranking out that attack ship, or they're calling in one from outside sensor range. Or you might be up against a low-level AI that doesn't have a weapon tech yet.
As for large ships with a ton of defense and no attack, they're dead meat. Defenses get worn down in later versions, and in earlier versions they can simply roll low. All it takes is one guy with a screwdriver to eventually take apart your unarmed, if well protected, ship.