we know that shuttlecraft can't pass through deflector shields
Sure they can, with a bit of trickery
We saw that in best of both worlds--but perhaps that was just an anti-transporter field, similar to the bridge field we see in ST II before the shields proper could be raised.
Personally, when I was watching TOS, I never even thought of the photon torpedo as having anti-matter in it. I figured that would be too powerful an armament to be allowed even on the battlefield after seeing the planet's atmosphere partially blown away in "Obsession." Heck, I even--being a child of the Cold War--thought of ( I didn't know the term drones) interstellar ballistic missiles between the Klingons and UFP.
Here I would suggest that we take (at least most of the antimatter) out of the equation
Here is a PDF that has a stunning photo you may wish to look at:
When watching Star Wars, I often wondered why the superlaser beams came to a point and did not cross one another. I figured there was some type of lens too small for the eye to see.
A decade or two later, they come up with a Bose Einstein Condensate.
Now we hear of Tibanna gas, and how the blaster bolts from star wars are really not as fast as the real thing from Wicked Lasers. So my guess is that the blaser doesn't fire a laser beam--but fires a gas laser apparatus itself
. A bolt of this gas wrapped somehow. The laser bean is bouncing inside a bolt of gas--then when this tibanna condensate hits, it discharges the laser bouncing back and forth directly into what it hits.
I would submit the photon torpedo does this too, but has better field manip' and maybe the BEC has just a hair of anti-matter for some reason. This explains why the phasers and photon torpedoes come from the lower sensor dome. it is one big emitter and does the wrapping all in that lower crystal dome somehow. Heck in Starfleet prototypes, they even have the back-up phaser above the tube--just the thing to explain the TNG Darmok episode..
For stun, you have this: http://en.wikipedia.org/wiki/Electrolaser