I installed 3.17 and unfortunately can't confirm if there is any change at all. If there is any change in functionality, it is completely inadequate to address the problem.
After doing extensive testing with tens of nuke hits, I have established that nukes get destroyed (both Tactical Nukes with the default CIV4UnitInfos.xml and ICBMs with bNukeImmunity = 0) in 3.17, but at a horribly inefficient rate. Something like 10 hits are required for 1 nuke being destroyed.
This rate is only improved by removing the Bomb Shelter building from the target city. It is not realistic that it gives much better protection for nukes than for other units (which are still destroyed after 4-5 hits). It also appears the hits are not cumulative for nukes as opposed to normal units. In other words, after 5 hits all other units are always destroyed, but after 10 hits only 1 out of 10 nukes are destroyed and it takes another 10 hits (on average) to destroy another. These numbers could be off by something like 20 % due to the work involved in better testing, but the chances are thereabouts.
If we assume that "Bomb Shelter" represents superhardened (25,000PSI) silos for the missiles, that should still only reduce the probability of kill from a directly targeted strategic 500kt warhead to something like 25% per shot (assuming less than 500 feet CEP easily achievable by ca. 1995 guidance technology). For tactical warheads it might be somewhat less, but not much since their guidance must be assumed to be better, compensating for lower yield. This means that after 5 hits all nukes should be destroyed in almost all cases, even if there is a Bomb Shelter in the city.
