However, that's when looking at Epsilon, Shockwave, and Quantum torpedoes. Velocity Shards and Plasma Thunderbolts are not like the others- similar to heavy missiles compared to regular missiles, they're much longer-range with a lot less punch. This makes them perform similarly to conventional missiles. In my opinion, they are useful as the secondary weapon line attached to the torpedo line- like heavy missiles, heavy railguns, heavy phase lances, and phase blasters. In other words, good choices for secondary weapons when you've invested in the according tech line. Of note, Velocity Shards are fighter weapons, though Epsilon has an easier time against ship armor (the whole point of taking torpedoes on fighters in the first place). However, there is some doubt as to whether or not these two weapons compare to missiles. Short answer: they are all-around inferior. If you want to heavily focus on long-range weaponry, Missiles are the right choice.
(Disclaimer: Fighters are always a good choice and you should get them around the time you invest in capital ships or earlier, depending on race... unless you have problems with computer performance and chose a galaxy your rig can't handle in late game. There are different situations that fighters and missiles aren't well suited for.)
I updated the relevant values in Es78's fantastic calculator and removed his theoretical accuracy (which was wrong, but almost everything else is on point). I chose Tier 4 (5 according to the spreadsheet, which is understandably incorrect), because Epsilon torpedoes simply far outperform Velocity, and similarly, Concussion outperforms Lighting. Then, Tier 5 sees Plasma Thunderbolts, which we'll look at further down. This chart assumes base weapon accuracy (no effect from targeting or countermeasures).
Hey! Its not fair to judge torpedoes against shields!
Actually, it is. Shockwaves do more damage against shields at close range- Epsilon does even better compared to equal-tier weapons. The bulk of most ship's resilience is shielding, and once a ship's shields are down, it usually won't take much more to render it disabled. And the ships with high enough shield regen (cough, SHIELDS) are the ones that can take a bit more beating before going down. Any ship that has more armor than shields is defensively weak and only fares better against railgun/phaser fleets. So, as usual, I proclaim that damage vs shields is the prime consideration for non-shield penetrating weapons.
Even accounting for space vs firepower at point-blank range (26 for M Velocity and 38 for M Lightning), Lightning still pulls equal DPS vs shields over weapon size. At 0 range. Nothing happens at 0 range.
What about Point Defense?!? Well, torpedoes are far more vulnerable to it than missiles.
Honestly, though, point defense is not so good at mitigating damage from seeking. If it were a single missile weapon firing, PD's effects would be noticeable, but you are never getting shot at by a single weapon, even from AI ships (not anymore, anyway). Ships focus on targets, and missiles/long-range torpedoes are good in battle because it is easier for multiple ships to focus on a target. You're looking at a single PD weapon mitigating damage from 2-ish incoming volleys out of 10 or more. IF a PD system reserved its shots for shooting at seeking (they're probably shooting fighters, which is really what PD is good for), it looks like this:
Velocity Shard: 2 torpedoes in 0.5 seconds, 425 speed, 58% weapon countermeasures, 37.237 raw damage at 1150 range.
Lightning Missile: 8 missiles in 4 seconds, 500 speed, 63% weapon countermeasures, 20 raw damage at 1150 range.
Sentinel Multi-Beam Defense v2: 4 shots in 0.4 seconds per 8 seconds (the 2/sec is for fighters IIRC), accuracy 81% initial shot, 16 damage
At the very hypothetical best, the Sentinel is mitigating 64 damage from seeking, but it's rarely doing that well. It does seem to split 2 pairs of shots between 2 targets. If both hit (doesn't happen often), the second hit is doing overkill against missiles. So, practical at best against Lightning is 40 mitigated and 64 against Velocity. In the case of Velocity, if all 4 shots hit, the shields are mitigating most of the remaining damage- making a Velocity volley effectively deliver 3.77 damage to shields (about 14% firepower getting past PD). With Lighting, that's 2/8 missiles down- 75% effective firepower. And then! Lighting fires less often; PD only gets a shot against mass volleys every 32 seconds against Velocity's 14 seconds. Sentinels are going to be firing almost on cooldown against Velocity attackers after the first volley or two, but only roughly 1/2 fire rate against Lightning.
So, out of those incoming 10 volleys of missiles, they're getting about 95% of their firepower through against a very lucky Sentinel. 10 volleys of Velocity are getting 83% of their firepower through an equally lucky Sentinel.
If you consider more powerful shields (like the Bubble Shields, let's go big and say T6 shields vs T5 weapons), this changes things up...
...well, not enough to really change the outcome. Lightning wins.
So, then, Thunderbolts vs Hive. They do better... lets look at T6 this time.
They're closer, but the Hive has almost the same range now. This accounts for base weapon accuracy and shield mitigation. Meridian shields at T6 only have 3 resistance. If we were considering Quantum Capacitors... but we're not going to, because the AI never uses them. Actually, why not, let's look at T8 Meridian with T7 Quantum Capacitors against T6 weapons.
To make the situation worse for the Thunderbolt, it is larger than the Velocity, while the Hive is the same as the Lightning. Even against T8 Meridian+ T7 Quantum Capacitors, the Hive matches the Thunderbolt's firepower against shields at a mere 660 range.
Still, let's look at PD's effectiveness again. PD scales well. Hive missiles are more resistant than Lightning, matching the scaling of PD. Thunderbolts, while their countermeasures improve, do not scale nearly as well. This time, let's compare a step up for PD, the Guardian Defense Grid at T7, at 2k range.
Thunderbolt: 1 torpedo every 10 sec, 450 speed, 62% weapon countermeasures, 74.4 damage @2k range
Hive: 16 missiles in 3.2 seconds every 44 sec, 500 speed, 67% weapon countermeasures, 26 damage up to 4.2k range
Guardian: 4 shots in 0.4 sec per 7 sec, accuracy 93% initial shot, 28 damage
The Guardian is still getting one round of shots in against a single volley, but it's easier for it to get in two rounds before a wave of volleys connects. Against the Thunderbolt, this is moot, since the fire rate is close to the same. It is easily getting in full fire rate against Thunderbolts, but still only 2 rounds (only considering concentrated attacks from 3 ships) in against a mass volley of Hives every 44 seconds. On the other hand, a connected Guardian shot is taking a Hive missile out with only a little overkill- but there are twice as many missiles in a volley, which fires more slowly.
So, at best, the Guardian is still only mitigating 5% of the firepower of a wave of 10 Hive volleys, with more idle active time between waves of Hives. Although a round of Guardian shots could practically defeat a lone torpedo, it still splits against a wave of 10 incoming torpedoes. 10 Thunderbolt torpedoes get 72% of their firepower through, and the Guardian is getting to work full-time. Again, if the Guardian is lucky, though it needs far less luck than the Sentinel did.
Missiles are 20-25% cheaper and are MUCH more effective against fighters. Torpedoes eat less energy and bombard harder. Of course, torpedoes punch through armor better... and that can occasionally be a boon before Meridian shields, but, IMO, armor is only of consequence when considering shield-penetrating weapons and fighter weapons (and that's fine).
So, the Velocity Shard and the Plasma Thunderbolt are objectively worse *primary* weapons compared to their missile counterparts.
While we're here, let's just take a quick gander at Quantum Torpedoes vs Reinforcing Swarms, with Quantum Capacitors.
). While 20% made it dies when focused fired by entries fleets worth of hives missiles. 