Was government-organized defense more effective or was spontaneously-organized resistance more effective at preventing this external enemy from achieving its goals?
Plus, it might not matter too much to people who rules them. If people don't see much difference between the two governments, then does it really matter that you were conquered. On the other hand, any conquering force would be a profound loss of freedom to an AnCap society. So there's more motive to defend. (For example, would Greek people care if France took them over? Maybe out of pride, but as a practical matter, there wouldn't be much difference.)
I don't know what "national defense" would look like in an AnCap society. But I have no reason to think it would be particularly difficult to come up with a way to do it.