Any nuke we would theoreticaly send at an alien spacecraft would be detonated manually, or on a timer. To do so it would have to punch into the outer hull thus making it's way inside of the ship. And yes we do have that technology, they are called bunker busters (they punch through the outer shell and detonate inside the building, we also use the same technology in the rounds we use for sniper rifles, but to a much smaller extent). So, in theory, we could destroy an alien ship with a single nuclear weapon.
While a ships hull could be made strong enough to withstand a blunt trama to it's shell (asteroid, space debris), in theory a piercing weapon could breach the hull. For instance, a metal mace justs dents metal armor, however, an arow will penetrate the same armor. The different is, while the mace releases it's energy on a larger area, the arrow releases the same amount of energy in a more focused smaller area.
And while a there is no atmosphere outside of the ship, there is most certainly some atmosphere inside the ship, thus making a pinpoint nuclear strike against an alien ship possible.
Low-orbit nuclear detonation was stopped by both sides in the Cold War for a reason. Probably didn,t want a huge debris field raining wreckage.(heh) Also,they were full of frozen civilians. Alsoalso, I don't think the arks were like an armada of warships. I picture (hate to name names) "Battlestar Galactica" minus the Battlestar.
When a nuke blast happens it sends out a emp wave so any thing like ship's are shut down no power runnig.
Why would all the ship's up there be empty?
For true, read the lore. Dem ships was held together with bubble gum and duct tape. (Not knocking duct tape)
The thing is ICBMs are not designed to pierce armor at all and even the ones that do use gravity for bunker busting on the ground, they would need to seriously redesign the warheads and let's face it using missiles which are essentially rockets launching from the ground is just impractical because they would see all the missiles being launched at them and from where as clear as you would see matches lighting up in a dark room and would reply in kind by lofting something down our way which is easier and faster for them being already up there in orbit, hell they could just launch large pointy rods as kinetic impactors which would cause as much damage as nuke minus the radiation when they impact, in other words things would have gotten nasty real quick and we would not have a dent which is why they never launched ICBMs at them.
The EMP is going to happen no matter where the bomb explodes. How much it affects the target depends on distance.
ICBM's have multiple warheads that split up during flight to make them harder to counter. Detecting them coming up from the surface of the Earth would be difficult because of their small size compared to the Earth and also there would be a lot of background clutter.
The analogy of the firecracker and the shoebox is flawed because for a nuke the firecracker would have to be replaced by a stick of tnt. Whether it goes off inside or next to it, the box is history.
You seemed determined not to accept the fact that ICBM's would be effective weapons against spaceships so I don't understand why you bothered to ask the question.
This all boils down to "What ship" - Anything currently built by current human tech? Toast.
But we are talking about Votan ships that we know next to nothing about, other than they traveled for 5000 years through deep space at relativistic speeds...and are HUGE. Thermal/kinetic energy can be managed (depending on the materials and what the ship was built for) and the Votan *do* have energy shields of unknown efficiency/strength. Equipment can be designed to withstand an EMP, and we don't even know if their tech is affected by a magnetic pulse to start with.
Basically, we don't know enough about the ships themselves to say either way. If detonated inside the ship and inside any defenses, I imagine the ship would fry without a ridiculous amount of redundancy. Outside? Can't say. Not enough information.
One think not mentioned is the high probability that the Votan ships would be able to shoot down, detonate, or re-direct the missles before they got close enough to be a threat. Even if the ships were "non-military" when planning for a 5000 year trip you'd include some measures to deflect or destroy space debris.
If you could get an ICBM close to the ship, yes I think you could do some decent damage, although your lethal radius would be alot smaller than when in atmosphere. A contact hit i believe would still cause significant damage.
However, throwing in another monkey wrench into the discussion.... Shields. Since all the grunts on the ground have some kind of shielding(quite effective in the case of dark matter). One would logicaly assume that ships prepared for a 5000 year space journey would have them too. How much damage they would absorb/deflect would have to be based on a guess at how strong they would be, and how effective they would be against a thermo-nuke.
Expert? No, just throwing my 2 script in like everyone else.