Now I know what you're thinking: 'Oh god, another Trek Rant.' The truth is . . . well, you'd be right. But I promise, this one will be much shorter. It also isn't nearly as polarized as my rant on the idiotic idea that Starfleet isn't a military organization. (Note: Remember to rephrase this in editing)
What I would like to proselytize to you about is . . . well, pretty obvious given the title. The idea that photon torpedoes (anti-matter warheads) would have no effect on shields only makes sense until you think about it.
Anti-matter is matter made of anti-particles. In essence, the charges of the particles are reversed. The protons in the nucleus of an atom of Anti-Matter are negatively charged (an anti-proton), and the electrons are positively charged (positrons). When particles of anti-matter and matter collide the mass in each is converted to energy, creating a mutual annihilation event. According to Einstein's famous E=MC Squared, that's a lot of energy.
So, obviously an anti-matter torpedo's goal (don't judge it; it was designed suicidal) is to deliver its payload to a ship, where the anti-matter would react with the matter in its target's hull, right? It's got a nice simplicity to it really. Make the target ship's own armor its executioner.
And shields, being pure energy would not create this reaction at all. Except one thing: a significant amount of the torpedo's own mass is made of matter. We see these torpedoes being handled by machinery and other people on a regular basis throughout the shows and movies. So we know the casing must be matter. There would also be no reason to make the drive, containment vessels, or energy source for the torpedo out of anti-matter. So we can be pretty sure that there is far more matter in an anti-matter torpedo than there is . . . annihilant?
Which means that a properly designed photon torpedo would release the same amount of energy, whether it impacted a ship's hull or its shields. We've also seen from virtually anything Star Trek that energy impacting the ship's shields does deplete them. Ergo, photon torpedoes deplete shields.
Granted, we'd still rather use the enemy's armor as part of the reaction, but its not necessary. Yet in more than one case in the movies and games the concept is forwarded that photon torpedoes do not harm shields.
On a guess, this concept was probably the result of a poorly thought out attempt to explain why Starfleet uses phasers at certain times and photons at others.
Thanks for reading my Trek Rant.