For me, Quantums will always be better than Photons.
Faster travel time.
Higher actual damage.
More burst potential.
This allows you to hold your torpedoes for the moment your target's shields drop, then get them to hit the hull before the shields come back up. You will not be firing the torpedoes as fast as you can, so you will never see the calculated "dps". To fire them so quickly, you would likely be wasting them against shields.
Besides, if you are flying anything other than an Escort, you will likely have some difficulty getting your target in the torpedo arc as quickly as a photon will refresh. This again prevents you from seeing the full dps.
Saying torpedoes have good DPS is like saying the M-16 has a rate of fire of 800 rounds per minute. Sure it does on paper, but in combat it's actually much lower because you've got to reload and stuff. The same goes with torpedo DPS, sure it can reach those numbers on paper, but in combat you aren't firing torpedoes often enough to take advantage of the DPS. Personally I never fire torpedoes unless I have HYT or TS ready, I'm sure that effects my DPS negatively, but it gives me better burst damage.
photon have higher dps than quantums and it is faster, not ther other way round. quantums are little bit lower on dps than photon but have a higher kinetic damage, they travel a little bit slower and reload time is 2 seconds slower. Personally i use quantums find it a balanced on dps and kinetic but sometimes on my sovy i use both just to have that caon feel og the E.
Both torpedoes have their places. Photons do more DPS if you can keep the launcher on target every time the cooldown comes up. Depending on ship type and build, this can be often enough that it would be worthwhile. Of course they also do the most DPS as long as your target has no shields facing you, which is generally not much of an issue in PVE. With purple projectile DOFFs, they also refire pretty much immediately if it procs.
Quantums of course hit harder and are more useful when you need to time a solid strike, like PVP, or if you have a ship that has a slow turn rate and isn't usually facing the target like a cruiser, so you deliver a big punch every so often with quantums then go back to broadsiding.
It depends on how many Torpedoes you have fitted. 3 Photons will out damage 3 Quantums, but 4 Quantums will outdamge 4 Photons. If you add in Projectile Duty officers then you end up with 3 Quantums out damaging 3 Photons. Even with Duty officers 2 Photons out damage 2 Quantums.For mines I find if you use 1 mine Photons are best, if you use two mines photons are a waste and as Quantums will do far more damage.
Above is ignoring High Yield or Torpedo Spread and is just for leaveing torps on auto fire.