Just because your connection is fast does not mean you will not have some lag or even errors in the data packet. There are always bottlenecks that may occur along the path to the server. I myself have a good connection but, in reverse to the problem your having, I have been hit or hit another when it looks as though the shots missed (happens alot with Nomad NPC BS). Just get used to it. It will happen again, i assure you.
Always you must think about, FL was never made to play in Capships or with multiple torp launchers. In addition to many custom hitboxes the game matehmatics will produce failures.
For example: You fire two novas and they are supposed to hit the target at the same time. Now it might be, they collide shortly before hitting the target and destroy each other. So you think to see a impact, but it isn't and the target only takes the damage of the explosion radius. Same for turret projectiles.
I think it depends all to the size of the hitbox and the size of the projectiles.
This is just an idea to explain the problem. It must not be really this cause.