I watched as some F-15I's dropped GBU-31(V)1/B JDAMs on an SSM TEL (facility 488 SSM Bn). In 8 attacks the SSM "SPOOFED" the JDAMs every time and caused them to all miss. In fact, I ran several flights at this particular target and had the same results every time. That "spoofing" might be possible IF the SSM Bn in question had any sensors or EW capability - oddly enough it has a Mk-1 eyeball only. Spoofed a JDAM? Really? That is a cute trick seeing as you must somehow block the reception of GPS signals, and a couple of other classified systems on-board the bomb. Pretty tough when the only hardware you have is a Mk-1 eyeball.
This sounds like a bug, but I haven't been able to reproduce it. If it's happening consistently on you, please provide a suitable pre-occurence save for investigation.
Moving on. I modified the same scenario and tried some nuclear attacks (same target) with a B-2 and B-83 (gravity) bombs. All I can say is don't try this at home using a strike mission. As the B-2 approached the IP, the aircraft dropped down to about 5000 AGL, despite being instructed to maintain military throttle and max altitude. To add insult to injury, the plane, after dropping the bomb (which is parachute retarded) circled around at low level watching for the bomb to hit. Result: one fried B-2 - and the B-83 missed the SSM TEL by 150 ft, so it survived. Right. I don't think a 1.2MT nuke miss of 150 feet changes much. I suspect the algorithm that calculates strike aircraft behavior is designed to only handle conventional weapon attacks - not nuclear.
Leaving this to Rag.
Finally I tried some Trident missle strikes. The MIRV sequence working was a pleasant surprise, the "malfunctioning" of as many as half of the MIRV warheads was rather odd.
It does sound odd. Our reliability figures for W76 and W88 are 80% and 85% respectively. Unless you were really unlucky, the working percentages should float around that mark. Again a (pre-problem) save would help.
The warheads getting fried by an EMP pulse was another oddity. EMP, usually only affects non-hardened systems, certainly not MIRV warheads.
Yes and no.
One of the things that a nuclear detonation releases is a high-energy neutron flux, at a relatively short distance (this BTW is the basis of the "enhanced radiation warhead" aka "neutron bomb"). RVs are hardened against it (partially because nuclear-tipped ABMs/AAMs use it as their primary kill mechanism) but they are still vulnerable to it at up to about 1-1.5nm IIRC, which is why fracticide is a real headache when allocating RVs on closely-grouped targets. (If you look closely when a MIRV bus begins deploying RVs, you will notice that the targeting AI prefers targets farther out from the primary [within the footprint constraints] rather than the nearest ones, for this very reason).
Until now we used the existing EMP wave as a placeholder for this neutron effect, but it is a rather overkill as you point out. Replaced it in Build 820 with a "proper" short-range neutron wave; you still have to worry about detonations close-by (either from ABMs or from "friendly" warheads going off) but you should no longer get distant effects.
The other oddity was the warhead missing the target by 300 feet, causing a miss! On an above ground SSM TEL no less!
Did it destroy the TEL regardless? Most anti-surface weapons in Command have some area effect (either purpose-built area-effect weapons like nukes, clusters, FAE, frags, airbursts etc. or point-impact HE ones) so even if they nominally miss the target there is a fair chance of damage depending on miss distance. (The message log is telling you that Nuke-1 missed by x meters and right after that Target-1 received a freaking huge blast wave and was wiped out; it doesn't tell you that said blast wave was caused by Nuke-1 going off). Again a pre-detonation save would help a lot.