Ave Cristiantine,
It was actually that thread that made me post this topic
Secret bases would allow you to save the space ship and eventually ripost to a nuclear attack, but MAD should be designed in such a way that will prevent the attack in the first time: the attacking civ will now that launching a nuclear attack will trigger a nuclear response on its cities in the same turn, before it have a chance to distroy enemy missiles or settle for peace after the attack. I think this is closer to the concept of a cold war.
The CTP related thread I was reffering to is
http://apolyton.net/forums/Forum35/HTML/000089.html
About secret bases, I replied in your thread.
Regards,
Remus