You need to think like the botters....
If losing one ship is critical, just add 4 more for redundancy. Seriously, I've been down this road before, with a different game as the main lib coder trying to overcome bots. You have to think like them and think, how would I do X, how would I do Y. What happens if he does this or he does that. As the defender, you have to base everything on... The botter always wins. He has more time to think and create ways than you have to combat. So, you think like them as above and install gates. Ok, so the botter can use the green and red light. Make the red light green. Make the red light blink. remove the red light. One light in 3D space means nothing. You keep adding gates and adding more gates. Eventually you end up in a situation where the botter gives up, or, you've made it so difficult that he has to continually change his bots to combat your gates. Which narrows down his performance and there of influence. If he's constantly writing/changing code to overcome your gates, he doesn't have time to use them