The vanilla tachyon lance used to be capable of shooting through fighters and missiles, but I think that ability got removed? I'd have to double-check and I don't have the game in front of me right now.
There's an old thing in the .WPN specifications, allowing for a Weapon to have a specific mask (see concept of a bitmask if you're not familiar with how that works) for evaluating collisions. I'm not sure if it's still working or Alex deprecated the code, however; I haven't messed with it in ages.
Essentially, you'd go into the .WPN / PROJ and write "pierceSet":["FIGHTER"]... I think?
I don't have a clue whether or not its actually used in vanilla like Wyvern said, but you definitely can always set any beam to pierce through fighters and missiles through editing its .weapon file. I do it in Archean Order for just about every beam since there are so many fighters. Beams used to be pretty suboptimal before I made that change. (Always would get stuck on the fighter cloud.)
Just set:
"pierceSet":[PROJECTILE_FF,PROJECTILE_NO_FF,PROJECTILE_FIGHTER,MISSILE_FF,MISSILE_NO_FF,FIGHTER],
in the file.
EDIT: Oh, and forgot to mention I don't think that code works for projectile weapons. Only beams, if I recall correctly. The closest thing to that for projectiles is the plasma cannon projectile file, and that forces your projectile to look a certain way so keep that in mind.