The photon torpedoes in SFC seem really disappointing because they tend to hurtle off into the ether, but that's just for playability: hitting all the time as in the show/films would make it too powerful. The game is also exaggerating the inaccuracy so that you can tell that you have missed, which doesn't apply to phasers because they always hit at variable damage (it does apply to most of the other direct fire weapons). If you keep in mind the extremely high practical scale that it's trying to convey, probably some tens of thousands of kilometres at viable hitting ranges, it's a bit easier to perceive as a carefully upscaled projection of what's really going on. Probably not quite that big actually - I'm remembering SFB, which has 10,000km hexes, minimum warp is speed 1, maximum warp with impulse is 31 (some simple maths shows that even that size is wildly conservative given the speed of light and reasonable turn times); I recall that SFC threw away the "always at warp" concept because it didn't line up with the source material.
On a more practical note, what to fire at what range is a useful concept to have in your head. All weapons have an average damage value which you can work out for a particular range, and a cost to operate - it's useful to fire at a range where the current weapon's damage/cost is high. The cost is both energy and time, and you'll find that by either measure photon torpedoes are significantly less efficient than phaser-1 at desirable combat ranges because the torpedo costs are so high: 2x as much time, 4x as much power. Photon torpedoes do pretty well at range 6+ because that's where phaser-1 starts to fall off, and (proximity photons) continue to do well at ranges 9-12 and fairly well beyond that. So you can snipe with prox photons at long range for a bit of attrition, and standard photons at medium range. In fact, photon torpedoes are also relatively efficient at very short range (1-2), so if you're going to overrun they're good to hold until you're closer.
What's been said about ECCM by various people is very sensible advice and is generally how the computer "cheats". Always be prepared to put a couple of points into ECCM. It is particularly painful with weapons which can miss because a small shift means you miss frequently. I didn't use ECCM for the first several encounters in SFC, despite both reading it in the manual and already knowing about it from SFB, because I just overlooked it as a cost with a very abstract benefit. Big mistake, and a nasty bump in the learning curve.
Missiles (drones in SFB) are of course extremely powerful because they don't miss or degrade - the terminator of munitions. If they'll do the job, you should definitely fire them; however they can be outrun, they are easy to catch in tractor beams, and they're easy to shoot down, so they only produce significant damage against energy-low ships. For everything else they are either a deterrent or a way to cost the enemy energy.