As the game stands in its original form (just with the weaponry modifications), I'd say Helios are really not a viable choice to be used en masse by capital ships. Unless the vessel were to charge in close enough to deliver most of its payload effectively (which would be suicide since turning away from a collision would be impossible at that point), it'd be a pure waste of money and ordnance. Taking the Helios' speed and the range at which capital ships usually engage, the attacked ship's point-defense systems and fighter escort would have plenty of time to intercept most of the torpedoes, unless an immense amount of them is used.
Beams still remain the best option, given they hit instantly, have far greater range, ammo is not an issue and they're impossible to intercept. I'd rather have twice or thrice the amount of beams on a warship than a comparable payload of Helios torpedoes. I'd assure you the enemy would go down before they even thought of launching their Helios stores.
Of course, if you think of more outlandish scenarios, like the one presented with Helios accelerated and shot at 500 m/s, you could also have rapid-fire, point-defense beam turrets that could fire and cycle through targets at lightning speed, intercepting them no matter their speed (torpedoes travel in a straight line, the environment's often empty space, and light's still pretty fast).