I use the Fallen Spire fleet, so I almost never need to use actual warheads for things. But I have used Armored Warheads, however that was WWAAYY back when their target priority was so low that the AI actually didn't shoot at them. I was still learning the game, only play with the vanilla toys, and didn't realize that it wasn't supposed to work like that. I used it like you would a Spirecraft Penetrater, slip it behind the AI's front lines and oneshot a high value target that I otherwise just couldn't take out. (Superforts mainly.) Perhaps a similar idea would work now? Rather than a slow, heavy armor warhead, make it a lighting fast, deepstrike weapon. Rather than a large aoe deathblast, make it either a single target shot, or plasma siege bolt on steroids. A very small aoe, but devastating to anything it hits. Very useful for eliminating single, high value targets, but rather useless against large numbers of smaller targets.
This could also be used to make the Core Warehead Intercepter more valuable to the AI, because right now its almost useless. Baring certain AI types you only ever see it on Core Worlds or AI Homeworlds. Give the Plasma Siege Torpedo its own damage type, make some of the average Core Guardposts immune to it, but leave some of the more brutal ones open to getting torpedoed into dust. Spread some Torpedo Interceptors around the galaxy, so that you can't just start blasting anything you want at the start of the game. Probably make it % based. All AI HWs and Core Worlds would have a 100% chance of having an interceptor, MKIV worlds have 50% chance, MKIII a 25% chance, and MKII a 10% chance. All Torpedo Interceptors will spawn near the command station. This means that on AI HWs it is protected by at least 1 Core Forcefield Remove Core Warhead Interceptors from the game entirely, and make all Core Guardposts, and AI Home Command Stations, immune to major electric. As Interceptors are fairly fragile, you could try using a Lightning Warhead to blow it up, then use Plasma Siege Torpedoes on the nastier Core Guardposts, but its going to cost a lot of AIP that way. Outside of some Core Guardposts, and perhaps the AI Home Command Stations, I would say that nothing else should be immune to the torpedoes. This way you could use it on the stuff that seriously needs to die as fast as possible. Like Mothershihps, Avengers, or Galactic Control Stations.
As for this possibly stepping on the toes of the new Lightning Warheads, give the warheads maximum damage that they can do to a single target and no armor pen, while Plasma Siege Torpedoes deal their full damage to everything in their small area and get max armor pen. Also, in keeping with the current theme that plasma siege weapons absolutely devastate shields, if a Plasma Siege Torpedo hits a shielded target, be it something under a stationary forcefield or something protected shield prjector, (Riot Shield Modules/Spirecraft Shield Bearers/ect) then anything within its aoe takes full damage, ANY shields in the aoe take full damage as well, and anything outside of the aoe but still in the shield takes 10% of the torpedo's damage.