On account of PVE, don't you think that saying "missiles are viable" and "if your goal is to have fun, then using missiles..." is a bit contradictory? And no, from, say 5 hardpoints, dedicating two or even one for missiles would cut utility or straight up damage of my firepower quite significantly. See, I don't need to drag NPC, at all. I don't need to destroy their guns, because when NPC loses more than 50% of it's weapons, it starts FDS charge sequence immediately. I don't need to disrupt their FSD, and more so, I would need to work around their PDs to use that missiles for utility I absolutely have no use for. In PVE, your only goal is to straight up blow up their ships, nothing else matters, and time it takes for you to do so, along with shutting down their defensive capabilities, with things like feedback cascade, is the only thing that matters. On "fun" note, I already use SLF on my PVE Krait, although it's utterly and completely useless in any combat situation, I still use it, because I don't have to sacrifice something significant, and it is cool to have SLF for me. But for using missiles, I would need to sacrifice helluvalot of DPS, which isn't worth it. I run Python with x3 Beams and x2 seekers, time it take to destroy targets almost twice as long as on my Krait.
There's your problem, don't use seekers in PvE when trying to kill anything other than an Eagle or SLF. Dumbfires are a much better weapon option as they have the third highest DPS of the C1 hardpoints behind only a railgun (rails are just nutty) or frag cannon (suffers against harder targets).
Edit: You're also using C2 seekers, don't do that, seekers suck unless they're a C1 for utility purposes or from a packhound launcher.
In my experience, NPC deaths from 0% PP have been very inconsistent. Can't count how many times, I reduced PP to 0% in CZs on Condas and other biggies at ~50% hull, and they didn't blow up, until their hull went to 0, me shooting at PP with multies all that time. Not sure if it's a bug with NPCs in particular, but I rarely go for modules these days because of it. x3 OC MCs with Corrosive and Rails melt away even thickest hull just a bit slower than they supposed to die from PP failure anyway, and I have much better combat presence, due to ammo capacity.
Sniping the powerplant used to cause instant destruction, but is now RNG based.
Now a powerplant has a low chance of exploding with every subsequent hit against it when at 0%.
Large alpha strikes have a vastly increased chance of causing a detonation, cannons, PAs or PenPayload dumbfires are nearly guaranteed to cause an insta-kill within 5ish hits against a zeroed PP.
Conversely, weapons such as beams or multicannons have a relatively low chance but make up for it through sheer ROF.
When flying small ships or fighting mediums and larges I nearly always target the NPC's powerplant.
I don't always kill them with it, especially if their armour is non-existent, but a substantial number do die with a large amount of hull remaining.
The key is to maintain the correct positioning so you have clear shots, then just keep pounding their PP until they blow.
As for ammo, a high capacity C1 advanced missile rack has 144 missiles, more than enough for most combat scenarios.
Side PSA: If you're having trouble killing Cobras with gimballed or turreted weapons, target their FSD, as it's in the very centre of the ship.
The auto-target point they normally use is just slightly higher than if you were to target the cargo hatch, meaning projectiles will miss if the Cobra accelerates upwards a tiny bit.
