The fix for #4666 to have caused some extra issues as of 41.13.
When nuclear missiles are involved, there are numerous fire reports that just don't show up - I think MM may be only displaying a report for the last weapon to fire. The end-of-turn reports and damage bars show that the additional attacks are being calculated and applied, just not shown.
When a (Santa Anna) nuke hits successfully, it is now doing standard Killer Whale damage to both the armor and the SI as per this report:
Capital Missile Bay at Naga Destroyer (Caspar II Control Ship) (WoB); needs 2, rolls 7 : - Direct Blow -
Killer Whale at Naga Destroyer (Caspar II Control Ship) (WoB)
Naga Destroyer (Caspar II Control Ship) (WoB) takes 50 damage to NOS.
190 Armor remaining.
Possible breach on NOS. Roll is 7: no breach.
NUCLEAR ATTACK! needs 9, rolls 9:
50 damage directly to the SI. 1270 SI remaining
Possible critical hit (Damage threshold exceeded); needs 8, rolls (5+1) = 6 : no effect.
Possible critical hit (SI damaged); needs 8, rolls (7+1) = 8 : Critical hit on Artemis IV FCS.
It looks like you have aero sanity on in your options. Could you re-test it without that? I suspect that some of the optional rules may be causing issues. It looked like it was working when I tested without many of the optional aero rules on. If it is indeed aero sanity, I don't know that it warrants another ticket. Aero sanity seems to create a lot of issues, and there are several tickets open already related to that.