1) Photon torpedos seems to move/fly faster, is that a visual effect, or they truly go faster?

2) The 25% torp bonus damage of the KHG set, is calculated to the base damage of the torpedo? or the dmg modifers and skills count too?

Witch one is right:

(Base Dmg + Torpedo Skill + Dmg modifers)*0.25
(Base Dmg + Torpedo Skill)*0.25
Base Dmg*0.25

I don't know which torpedoes are the fastest in the game, but I do know that photons are much slower than quantums.