As gr1mre4per said there are essentially two different ways that destroyed capships are implemented. On the one hand, you have those capships that function normally, and can be destroyed - and on the other, you have capships which are implemented in the already-destroyed form.
Funnily enough, by the way, even though WCP uses an already-destroyed capship in the very first mission of the game, they never bothered to fix a major issue with the depiction of already-destroyed capships - namely, that the very first thing they do when you see them, is die, with a big explosion, and even (if someone was daft enough to give such a capship the wrong pilot) death comms. The same problem shows up later in the game when you fly past an alien comm relay station you'd destroyed in the previous mission - and once again it starts by exploding. You'd think that it would have occurred to them that if you want to show a ship that was already-destroyed, it shouldn't start by dying, but - oh, well.
Anyway, so yes - the minor explosions are generated randomly at the hardpoints on the main capship hull. I disagree about hardpoints set to 0,0,0 being a problem - it's fine, because usually you'll only have one such hardpoint (multiple components can be tied to one hardpoint), and usually it will be hidden away in the middle of the hull. Just make sure to have plenty of other hardpoints. In fact, it's often good to add some hardpoints to a capship that are used solely for explosions.
The big problem with capships (live ones, that is), is the limitation imposed on the destructible meshes by the existence of turrets, and the fact that turrets are not tied to components but rather to the main mesh. Essentially: while there's nothing stopping you from having a capship that consists entirely of destructible components, with no real main hull (like we did with the Targu II frigate in Standoff), if such a capship has more than one component, you're going to wind up with the rather silly situation where you've got active turrets attached to a destroyed part of the ship. Worse still, if you decide to really warp the destroyed mesh, those turrets might be floating around in mid-air. It's a nuisance, because of course, the main hull doesn't get replaced with a destroyed version - not even a texture change!
It is for this reason, destroyed capships in WCP are always fundamentally so unsatisfying, and it is for this reason that on the one occasion where they really wanted the player to take interest in a destroyed capship (the first mission of the game), they implemented a special already-destroyed version with far more visible damage than you'd normally see killing a capship in the game. We also did this in UE with the Intrepid, having a separate version of the ship show up in the mission where you inspect the wreck - but if I recall correctly, we didn't make good use of this opportunity. Apart from adding a bunch of hardpoints for extra explosions, I don't recall us making any significant changes to the hull - I think even the textures were more or less the same, just with darkened engines and stuff. I'd love to see a really good wreck of the Intrepid to put in the game.
Come to think of it, hypothetically, it should be possible to actually use far more interesting destroyed capships in the game with the aid of a simple trick - the moment the last component is destroyed, deactivate whatever capship is there, and in its place activate a specially prepared already-destroyed version. In that case, the initial explosion would actually work to the game's advantage. Could be quite an interesting thing to try.
