It might make sense to use missiles more freely in the early early game, so don't take it as a hard rule. It is still always better to shoot a missile then to take damage. But once you get the ~90 scrap to get level two shields you should rarely need them until sector 3 or so. I judge based on enemy weapons. If they are shooting missiles at me, I will shoot missiles back the second my laser whiffs, because shields are ineffective against missiles and that is something I want to put an immediate end to.

You do get a number of missiles for free throughout the run, and there's no way to sell them directly aside from chance trade events. Just avoid needing to buy them, and keeping the option open to choose fuel in events where you have a choice.