Starship combat often ends quickly because small starships (fighters, patrol boats, light freighters, etc.) can't take much damage. In addition, all or most of the player group tends to be in a single ship barring games that use starfighter groups. So, one target kill by the NPCs could take out the entire group (even if it doesn't kill them). With laser cannon, this is usually a few turns of give and take, but when concussion missiles or proton torpedoes come out, the situation gets crazy.
There doesn't seem to be a good reason for a fighter not to use its concussion missiles/proton torpedoes against small ships in the first pass. These weapons outrange most other weapons mounted on small ships, and they allow for quick kills. This is vitally important when your own vessel is unlikely to survive more than one or two hits. So what's the downside to using these weapons?
The first is the Limited Ammo. This isn't really a downside. Your vessel isn't going to want to be in the fight long enough to run out of ammo because you'll likely run out of HTT way faster. As for the cost, even proton torpedoes are peanuts - 750 credits each means that firing the Linked 1 pair is going to cost you 1,500 credits. To put it into perspective, that's what repairing 3 HTT would cost, and it's a small price to pay to keep them from shooting down your 30,000+ credit fighter.
Slow-Firing 1 is the big downer. This means you'll need to do something else on the turns you're not firing your concussion missiles/proton torpedoes. Either go with lasers or try like hell to evade, but you're likely just spending the turn waiting for the next opportunity to ace some bastard with your next missile/torpedo attack.
But wait! What if the target is "Spoofing" Missiles? Well, they had better be. In fact, every ship with an extra crew slot needs to have someone that does nothing else. This might even be the best use of an astromech droid for fighters that have them. Still, an extra upgrade or two won't matter all that much against most enemies if your Agility/Gunnery pool is looking good.
So, anybody up for Rocket Tag?