All things being equal, beams are superior to torpedoes, for the simple reason that beams cannot be shot down, where as torpedoes can. In addition, beams are generally faster than torpedoes (unless you have some sort of warp-speed photon torpedoes like in Star Trek). Which brings me to my point - all things are not equal. In real life, missiles displaced guns because of their inequality - missiles are just as fast as guns and much, much more accurate. And they can be carried on tiny torpedo boats and even fighter craft. In FreeSpace, beams are superior to missiles - at least, the ones we've seen. It might be something that the only capship-destroying weapons on fighters are bombs, not missiles, and slow and easy to shoot down.
And then there's the whole ECM thing ... and CIWS ... Nothing is black and white, and in science fiction, weapons are only as effective as you want them to be. Look at WC capships vs. FS ones, for example. Or SW's hundreds of turbolaser batteries vs. ST's few, large ones. I'm not trying to create a vs. debate, just showing the inequality of it all. Because in combat, inequality - called superiority - is what wins battles.
