Greetings from Charlotte.
You asked about hacking. Hacking imho is unauthorized changes. If you aren't actually inside or online with the target system then you can't hack it. Physical damage is probably closer to sabotage or vandalism.
There might be one other possibility tho. I am assuming since you said LED that both factions are using electrical based architecture. These are subject to Electro-Magnetic Interference. Unless properly shielded or designed to accept and safely deal with incoming EMI, Electrical systems can be hurt pretty bad pretty quickly.
I liked your idea of using the lighting. I don't think Ive ever seen that one used before. Isnt it always a dirty trick tho to blind the other guy so that you can gain an advantage? Lighting would be tied in directly to the entire ship and accessible from anywhere. Allthough they are probably branched or noded. You might not be able to kill the engines using the LEDs but you certainly could divert a lot of brain power to the problem of solving it.
One way that you could hack the other ship is by using an infiltrator. Someone working for you but on the enemy ship. Assuming you could successfully get someone from your side that far, they would probably have enough knowledge of their language, habits, and systems to at least access the point of entry. Whether they understand how the virus works doesn't matter.
There's also fuel. You could "hack" the engines by sweetening their fuel. You could also rub Vaseline on all their windows
What would happen if instead of killing that other ship, you forced the gas pedal all the way to the floor in such a way that they could never stop accelerating? See ya, wouldn't wanna be ya!
I think its a wonderful idea to have two factions on the same planet
I think its incredible that they both have developed space ships technology without one having destroyed the other first.
Cheers
(A)