All true. But a hypothetical 2000 damage energy torpedo is half as powerful as a Reaper against armor and twice as good against shields, and we deal with Reapers all the time. The balancing levers you pull are ammo, OP cost, delivery methods, ease to shoot down, etc. The damage itself isn’t the only factor to consider. Honestly, if you do take a hit on hull, this torpedo does less damage than any other finisher except a Harpoon. So, even when it does hit, you’re not getting the same “oomph” as the others. The trade off is that the shield hit might cause an overload.
As long as the other balance levers are in place, an energy torpedo (to me) is no better or worse than an HE one: it has its own pros and cons.
I'll point out a hypothetical 2000 energy damage torpedo is theoretically 1/4 as powerful as a Reaper against armor since 4000 high explosive * 2 = 8000 (2000 vs 8000), not half. However, Reapers are ludicrous overkill against any armor in the game, even a fully kitted Onslaught XIV with officer. Any ship taking a Reaper to armor will have 0 armor left in that spot. As Thaago said, 2000 armor damage will pretty much leave any cruiser not named Dominator with 0 armor in a single hit, along with half the capitals.
A 2000 energy damage torpedo is equally good against shields as a Reaper since 4000 high explosive * 0.5 = 2000 (2000 vs 2000), not double. It is also equally good as a single Sabot (200 kinetic*5*2 = 2000), but given the 3 to 1 ammo and no non-linear effects against shields, makes it about 1/3 as good (probably less if it's a true unguided torpedo) as a typical set of 3 Sabots.
So, we've already hit the first balancing point, which is what job is a single 2000 damage energy torpedo filling? It's straight up less effective than a Reaper if there's a 1 to 1 correspondence in ammo for these things (armor penetration is essentially equal since nothing in the game has 5000 armor, hull is half, shield is the same). So do we field them like Hammers? 2 to 1 ammo? Then when considered in aggregate, said energy torpedo two pack is essentially twice the armor penetration, same hull damage, and twice the shield, at the very first adjustment to ammo. So ammo perhaps a too coarse balancing knob.
Do we make them not torpedoes and turn them into some kind of guided munition like Atropos with 1 to 1 ammo correspondence with Reapers? That's also is pretty coarse balancing point, since as soon as these become guided, you run into the mass Harpoon style situation - but fired at the start of combat instead of when something gets overloaded.
You're basically down to how hard this thing is to shoot down or dodge as your balancing point, which is difficult and somewhat nebulous. Overall it sounds like something hard to balance to me. Not impossible, but really hard as you're trying to find some use case that doesn't lead to simply replacing Reapers, Sabots or being strictly worse than either. We've already got Reaper vs Hammer in the unguided armor opening space. Single big hit sabots were considered too strong at 750 kinetic (21 times less penetration than a Reaper) and split into the current EMP + split shot version with 80 times less penetration.
My experience with guided energy missile equivalents to Harpoons (even with damage significantly reduced from 750 energy) in tournament is they're
openers, whose punishment for not taking it on the shield is it's a
finisher. They really are mostly competing with Sabots. And ships on the receiving end either overload due to being forced to take it on shield, or take hull damage immediately because their armor is gone. Or more usually, 10 of these come in and the ship overloads
and blows up, since the excess beyond shield overload isn't wasted at all when it hits armor and hull. Just spam one missile type until dead. Or they get toned down the point where 10 of these don't overload shields. Again, the hard to balance issue.