Nukes are actually more destructive in space than on Earth
(As an aside, first I'd like to tell you that a nuclear fission reaction typically is over within 100 "shakes," a shake being 10^-8 seconds, so that means the whole fission reaction takes about a microsecond. A few milliseconds is plenty of time for that.) Now, onto my main subject...
Earth has an atmosphere, which absorbs a great deal of the energy from a nuclear explosion, reducing the damage dealt. In space, you get hit harder because you don't have the atmosphere to shield you.
What you get hit with is neutrons and photons instead of an air blast, but when the neutrons and photons hit your ship, it goes boom. Specifically, the radiation penetrates into the hull of your ship and heats up the metal to the vaporization point instantaneously. It also instantly melts a lot of the metal that's too deep to actually vaporize. This vaporized and melted metal rapidly expands, causing a shockwave, which spreads through the ship, smashing things. It's as if someone had strapped a large amount of dynamite to every square cm of your hull on the side facing the nuke, and detonated it at once.
In addition to the shockwave, the vaporized metal explodes away from the ship, which causes a very sudden and powerful reaction force on the whole ship, like a rocket engine - indeed, like Project Orion. This extremely sudden acceleration breaks things all over the ship, if you don't have a huge shock absorber facing the nuke like Project Orion does.
Since you thought space nukes were less dangerous and linked Project Orion in support of that, I should tell you why the nukes used in Project Orion wouldn't destroy that ship, and it's not because the ship's in space. First note that Project Orion would use the nukes to climb out of the atmosphere as well as in space. Second, nukes are powerful, but a few meters of steel goes a long way to withstanding them. Project Orion has a huge pusher plate that protects the back of the ship. The other sides of Project Orion aren't so protected. Third, Project Orion has an enormous shock absorber between the pusher plate and the main ship, without which the extremely sudden acceleration would be breaking the ship even with the pusher plate. The shock absorber is a large fraction of the length of the ship. And fourth, the nukes used in Project Orion would be small fission devices, not the huge thermonuclear weapons I'll be talking about.
The DNA damage from radiation is also much, much more dangerous in space than on Earth. If Earth didn't have an atmosphere or the ground/buildings to protect us, the 50 MT Tsar Bomba would have irradiated every single human being on the planet; a person 12,742 km away, on the exact opposite side of the planet, would have received around 1 Sv dose, which is possibly fatal. That's what happens in space.
So I'd like to frame challenge by considering what happens if a big nuke does not penetrate, but just explodes nearby. It could easily destroy the alien ship or kill everyone inside if their ship is not sufficiently prepared for such an event.
We're serious about trying to stop those aliens and they do have a really big ship, so let's imagine hitting them with a "Big Nuke" detonated 1 km off to the side. The weapon we'll be thinking about is a 100 MT (4.184 * 10^17 J) thermonuclear weapon - the original design yield of the Tsar Bomba, if the Uranium tamper had been included. I like this because 100 MT is a nice round number. I'll go ahead and show you some example calculations so you can adapt them to your setting and decide whether the aliens can survive it.
First, the explosion damage. The ship will receive 3.3e6 J/cm^2 of neutron and gamma radiation. Converting, this is about 800 grams of TNT per cm^2, or 8000 kg TNT per m^2.
You indicated the ship is 431m long; let's suppose the hull area exposed to the blast is 400m * 200m = 80000m^2. This would be the equivalent of 640,000,000 kg TNT strapped directly to the hull and set off.
Could the alien ship survive this? This is more of a judgment call, but it's unlikely.
I've done a calculation indicating that if the ship has a steel hull, the top 10 cm of steel will turn into vapor, and the atoms in the vapor will have an average speed of 8000 m/s. All those atoms will practically instantly go flying off to the side, and from conservation of momentum, the rest of the ship is punched the opposite way. If (and we're being very generous here) the rest of the ship masses 100x more than the vaporized 10 cm of steel, that means the rest of the ship would instantly be moving at 80 m/s after the punch. Any humanlike aliens inside the ship would be killed by that, when the wall hits them at 80 m/s. Crash couches wouldn't save them. Plenty of equipment would be destroyed by the sudden g-forces as well. The hull, also, would cave in and cause massive damage, even if it was meters thick.
One possibly useful comparison is the Mark 48 torpedo. This torpedo has a 293 kg warhead, which it detonates under the enemy ship to break its keel. In other words, just like our nuke, the Mark 48 doesn't penetrate, which is why it is a possibly useful comparison. Clearly, the Mark 48 delivers many orders of magnitude less energy per m^2 than our Big Nuke does.
Another thing to consider is, how much of the hull would directly melt or vaporize because of the heat from the radiation? It's a bit of an involved calculation; we may use the number that an inch of steel reduces radiation intensity by about 50%. The heat of melting for steel I take to be 700 kJ/kg, and the density of steel is 0.007859 kg/cm^3. The formula I came up with is: 0.272893 e^(-0.272893 x) * (energy deposited in units of J/cm^2) / .007859 = 700000, with x being the depth of steel hull in cm that will immediately melt. For our case x = 19 cm. So steel plating will be directly vaporizing or melting to a depth of 19 cm. Of course, most of the damage will probably be from the shockwave and the whole-hull stresses, not the direct melting.
Next, we can check how much radiation shielding the aliens would need to avoid dying from irradiation. Based on slide 15 of this slideshow, neutrons are far more damaging to the human body than photons for a given energy, so we can ignore the photons for a ballpark estimate. The neutrons that would deal most of the damage would be high-energy 14 MeV ones from the fusion reaction. These would be a fraction of the yield, certainly less than half (half of the Tsar Bomba yield is from fission). Let's say 10% of the yield is 14 MeV neutrons. Based on the chart from the slideshow, 14 MeV neutrons deliver about 450 pSv cm^2 of radiation dose to the human body. This means, if you are hit with N neutrons over an area of A square cm, you will receive 450 * N / A picoSieverts of radiation dose. If you get more than 1 Sv dose, you may die.
This radiation dose is in terms of number of neutrons, so we need to convert to Joules. Each neutron has 14 MeV = 2.243 * 10^(-12) J of energy, so the dose per J/cm^2 is 450 pSv cm^2 / (2.243 * 10^(-12) J) = 200 Sv cm^2 / J. Multiply this by 3.3e6 J/cm^2 * 10% and we find that an unshielded alien would receive 6.6e7 Sv.
To bring this down to a safe level we need to add radiation shielding. From this article, 30 cm of concrete will reduce the radiation damage by 90%. The alien would need 8 layers of that - 240cm of concrete between the alien and the blast - to bring the dose below 1 Sv. It would be more efficient to use lead. From this blog, the radiation halving thickness of lead is 0.4 inches, or about 1 cm. The alien would need about 26 cm of lead.
You can decide what this all means for you. Really the hardest part would be getting your nuke within 1 km of the enemy. Why wouldn't they avoid it? There are ways you can make the nuke stealthy - you can put it on a ballistic trajectory (no thrusting) with angular radar-reflective surfaces, like a stealth bomber. But this will only work if the enemy also travels in a predictable trajectory without thrusting at all, which they wouldn't do if they expect any trouble.