Weakpoint
Those large reactors are unnecessary and nowhere near being fully used, the missile factories are far away from their launchers, ammo factories are far away from everything, truly excessive number of energy storages, no engine rooms, and top missile launchers are still hitting the ship. The entire thing is over-crewed and has too many reactors. Read 0neye's guide.
Also, weapons can't focus fire.
Try fighting this on AI vs AI, improving your ship while keeping it under budget until you beat it:

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Nuke launcher is unnecessarily far away, two tiles of corridor is about as far away as you want it without it being too crew intensive. Engine rooms are underutilized. Is you place the ammo facts adjacent to the nuke factory you could easily support two launchers from the adjacency bonus. Flaks can work with one factory or two factories at +25% each feeding two flaks fairly well. Your single nuke launcher is essentially your only fire power. Try running your ship off of two mediums instead of six smalls, if possible.
Try fighting this on AI vs AI. 