Yea I figured that might be the case. Mainly though I just wanted them to cut through ships causing damage along the way, then coming around for a second assault either on the same target or on a different target all together, but this time actually exploding on impact.
The MoveThruTarget line seems to be the only way to get close to this, but the only other thing that is missing is a particle effect for when the drones rip through the target, for example a small explosion or a bit of small debris as they move through the Hull. If an effect could be created or an already existing one added to give a visual cue to the fact that the drones have just penetrated and exited a target, then this would still be awesome.
Again, a cue for another particle effect before the weapon hits the target would require Sins' coding to be changed. If you use the MoveThruTarget line, you'de still have to do this, only this time you'de have to get even more coding to tell the drone travel effect to disappear on the second impact.
Maybe we're thinking about this in the wrong direction, what if we could configure the ships bombers to do some sort of kamikaze style attack. With the right models and particle effects it would probably look more true to form. The time it would take to build new ones after each attack would be comparable to the time it takes to wait for anti-matter to build back up.
I don't think there's a way for a strike craft to... do what I think you're imagining. If you're imagining a targetted ability, which sets the strike craft to target a ship, go through it, then swing around and hit, this would still require coding changes. Along with this, there is no ability type that cannot be turned off autocast that targets single ships to my knowlege PLUS the fact that when you're not in combat, you'de have a load of drones following your ship. There is also a code that slows down the rate of production on strike craft whilst in battle.
There's not much point in doing this amount of coding, let alone trying to get codes for the actual game which aren't avialable and probably way to complex, for just a drone. I think the best you can get without doing any complex coding is just make it, like a phase missile, have a good chance of passing the shields.
When or if they release Sins of a Solar Empire 2, it will probably have more complex coding, which means more modding tools, to do this since (I think) they only had a $1m budget on this one.