No idea if there is a connection with bomb shelters, though the cities I nuked definitely had none.
how do you know this? the bomb shelters may have been destroyed when the nukes hit.
I used a bit more then 100 nukes on 50% of a large great plains map. The last radiation was definitely gone 10-20 game turns (epic or marathon) after the last nuke drop. So yeah, it was a complete waste of time, as I was hit by desertification as hard as the others. What pop they lost due to the nukes, I lost by starvation.
how in the world were you able to stockpile so many nukes without ruining your economy? if you had that much extra mfg capacity why didn't you convert it to research to win the tech tree race and then to SS components to win the space race?
in the Better Tomorrow mod nukes are more expensive than cruise missiles, and in my opinion not nearly as effective if you know the enemy has built SDI and likely bomb shelters. only one in four hits with SDI defense and at that it only does 25% damage if protected by a bomb shelter. you would have to target 16 nukes on one city to have any statistical odds of a complete kill.
in contrast the 16 cheaper cruise missiles will reduce 16 full strength units by 50 to 70%. of course the downside it that their range is only eight tiles so you have to be near enough to use them, likely already at war.
in my current Better Tomorrow mod game playing as Japan Spain's nuclear gambit failed miserably. China rapidly built SDI and later used nukes to damage one of Spain's cities. it was partly Spain's accumulation of nukes (seven) that prompted me to build an invasion fleet near Spanish soil. that in turn caused Spain to overreact and declare war. interestingly enough they then had to wait for me before launching their nukes. I could not of course stop their nukes (even with SDI), but I captured one of their cruise missile cities before they could launch one of that type of missile from it.
this is one of the few Civ 4 games I have played where the AI went the nuke route instead of beelining for a SS victory. Spain had previously had an inconclusive war with neighboring China and also saw that it was behind in game stats to both China and Japan. apparently feeling vulnerable to attack, rather than building up its economy it decided to go nuclear.
the only way a nuke strategy can work is if all your opponents have relatively no research or mfg capacity. otherwise as soon as a potential nuclear agressor builds the Manhattan project all of his likely opponents (those with any decent mfg capacity) will built SDI and bomb shelters before they can ever launch a nuke at them. in my current game I believe China built SDI before Spain did although the latter (as it turned out) wasted resources building the Manhattan project.
if you have that much of a mfg and economy advantage over your opponents, then a nuke strategy is unnecessary anyway. you can win either with a domination, time , or SS victory.
=============================
discusssion regarding victory conditions, now that the topic has been raised ----
I have already disabled time and culture as victory conditions in my own Civ 4 games and am now inclined to also disable the spaceship victory condition.
what follows is a description of my current Civ 4 game and why it has led me to want to disable the SS victory condition.
all of which is my windy way of saying the SS victory means nothing in terms of who potentially can control territory.
in future Civ 4 games I think I will set domination and diplomatic as the only victory conditions. otherwise the AI inevitably goes for the SS win and so usually researches artillery to bypass the need to research flight (and hence develop a strong offense/defense).