First, it helps to know stats of the units. A nuke missile from a strategic missile launcher (and Sera Battleship) does 70k damage upon detonation (+500 dmg) and a sub nuke does 25k (+500), and does this much damage in a large AoE, a tiny bit wider than the yellow targeting ring. T3 shields absorb about 15k damage (13k cyb ED4, 14k cyb ED5, 15k uef, 18k aeon, 21k sera) and cost between 2400m to 3600m each. T4 nuker damage? Fahggetabouddit, this doesn't apply to that.
The discovery: If shields are stacked around something important, say a Mavor, Paragon, or Salvation (Rapid fire Arty), Yolona Oss (Sera T4 nuker), the shields may protect it from a nuke if the nuke was not aimed directly at it or in a spot under the shields.
Thoughts: I find this kind of fascinating, since it makes me realize how the nuke weapon effect works. It seems to work like the T4 nuker, except much quicker, in which the damage seems to radiate outwards from the center of the impact. I wouldn't classify this as a bug. This is just a FYI, since this happened to me in actual games. I nuked someone's base or firebase and somehow their ACUs or Salvation survived, yet everything else was flattened, and this left me boggled. At first I suspected that maybe a certain faction's nuke was gimped, or maybe another faction's nuke was more devastating, so I decided to do a sandbox game to test and understand it better. I wouldn't classify this as a bug, but more as game mechanics made to mimic a a real life nuke maybe.
Test process: I made a sandbox game with an AI. I spawned myself a paragon and got rid of the enemy ACU to prevent him from doing something annoying. I spawned 2 of each faction's nuker and let them build. I then created a sort of targeting ring, and copied and pasted it in other parts of the map to act as a test and ensure that each nuker was equally devastating, as indicated as the unit blueprints pretty much being identical. I then spawned the AI a paragon, 10 energy and mass storage units. I then spawned 2 rows of T3 sera shields, one row of 3 and another of 4, for the AI. 4 is enough to stop a nuke, but 3 is not, but there were 7 stacked altogether, which is more than enough to stop a nuke. My first nuke, I launched just barely outside of all the shield domes. My second nuke, I launched just barely within one row's shield domes.
Result: The shields completely stopped the first nuke. The nuke did not go through the shields and wipe out everything underneath. Even units part of the targeting ring that were under the shields remained intact. I'm not sure if the ones that were not covered by at least 4 shields were protected or not, but it seemed like more survived than I expected. The second nuke wiped out the shields, mainly because the 500 damage portion of the nuke goes through shields and the shield generators themselves only have 600 hp, but a lot of the units part of the targeting ring that were protected by the shields survived yet again.
Lesson: if you want to kill a Mavor, or whatever, with a nuke and it's protected by lots of shields, target it directly or at least notice the orientation of the shields. Do not expect it to be destroyed if you're used to everything within the yellow ring to be blasted and include it as a target, on the fringe of the yellow targeting ring.
Application/challenge: About to be nuked? Your ACU have the T3 engineering suite? Quickly spam enough T2 shields to save your sorry ass when you hear the strategic launch message. If you can pull it off...
Replay attached, for your viewing pleasure.