Option 3: Make autocannon rounds explosive. If missing the target, they explode is a flashy flak cloud. Problem solved

As for inaccuracy, remember that the distances in this game are humongous compared to those in modern day earth combat. Despite shells traveling quite quickly, the time it takes for them to travel through all that space, the target might've shifted heading just a little bit and thus, by the time the round gets there, you'd miss.
As for lasers, they dissipate as they lose all their thermal energy the further they travel in the coldness of space. Missiles should explode when running out of fuel, but they have guidance systems so they generally hit anyway.
I agree with Major Stress though. I'd rather these physics be kept as simple as possible for the sake of stability and fun. There are many other ways to make firing, combat and flashes more appealing. Eye Candy for the win.
The little bit that's on topic:
Yes, fighters do travel through planets, I checked last game and can confirm it. But this is being fixed or has been fixed internally if I'm not mistaken.