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Is there any defense for cities against ICBMs? Shields do not seem to help and I am unable to determine if bunkers help mitigate damage to population or structures from nukes.

I have found that the radiation aftereffects can be combated, but the effort is enormous and time consuming. My current doctrine is to build bunkers up as high as I can and to build at least a level 2 radiation cleaning facility in each city BEFORE a war. There are two other types of anti-radiation facilities, but I have not worked with them much. Also, I put some solar energy facilities near the city for energy, This way, after the city is nuked, energy for radiation cleanup is available and it can be started immediately, in case a big reactor got taken out.The higher up you can build the installations, the faster you can recover. There is a race to be won as the population flees the city due to radiation, so a recovery needs to be fast enough to occur while there are still people available to man the cleanup facilities. In the meantime, mothball most everything else to focus workers where needed most and hope you can recover before all the industry disintegrates due to lack of workers and hope the radiation can be reduced fast enough to entice people to stop leaving.

Thoughts, experiences and solutions earnestly welcome.

NOTE: my observations are based on several games, most recently when my 5 oldest cities were blasted with nukes over a 5 turn span. Two cities were hit twice. The Republic of Mordor suffered greatly to bring you these observations.

Some background comments are warranted.
Normally one tends to concentrate production to take advantage of economies of scale that are built into the structure progression tree. In nuclear war this can be bad. If you have only one or two centers of production of an item, say ammunition, and they get blasted then you can be in real trouble very fast. I have found the most serious and far reaching bottlenecks to be energy production and transportation. Ammo is up there, too. So counter to normal considerations, decentralization is your friend. If you have only one or two big energy producers and they get nuked, bad time are near. That is why I suggest at least some local energy production ( solar) in each city. And, unless I have just been unlucky, the AI is smart. It seems to go after my weak points, within the limits of whatever reconnaissance Vic has built in.

I forgot to mention, when building solar at your cities it is wise to put some of it OUTSIDE the city so that it does not get blasted. That way it can function so long as sufficient pop remains.

I don't think there is any viable defence against ICBM attack.
Bunkerization and anti-radiation infrastructure can help mitigate the effects of a nuclear strike but they can't nullify the impact. Further, they only defend the local hex so every major city and every important logistics node needs them. Worse, the attacker can simply keep attacking in response to an initial strike being less effective.
When I lost a campaign to ICBM attack I was being hit by three ICBMs every turn and I only had 5 or six major zone cities. So in a 5 turn span a single major city might have taken 3 ICBM hits. Under that kind of sustained attack the radiation levels on the city hex can exceed the levels that anti radiation infrastructure can help against. Add that to mass casualties from the blast effect and the zone is likely in a state of total collapse. Damaged buildings stop working the number of available workers plummets. Inter zone logistics collapses, and the army starves in the field. Even the resource stockpiles in your SHQs can be destroyed with ICBM attack.
A strong decentralized empire could certainly recover from a limited nuclear attack, especially if mitigation measures were in place before the attack occurred. But that doesn't matter because, unless the army was in a position to immediately destroy the enemy ICBM launchers (unlikely given ICBM range is unlimited), the attack will not be limited. Multiple ICBMs can continue to land every turn until the enemies war stock of nuclear material is depleted - something you'll have no idea when or even if it will occur.

Yeah. What you said.
I was fortunate and was able to retaliate fast enough in one game to slow down the missile rain long enough to get ahead of the other side. I still had 8 or 9 cities nuked and saw well over half of my army melt away. It was a darn close run thing.