If you attack a huge ship with cluster missiles, can you use the bonus attack to shoot the other section?

No, it's not a separate target. Btw 2nd edition huge ships have a single base, not two, like 1st edition did.

Exactly. However, you can absolutely target any enemy ship in Range 1 of the Huge ship, which is a gigantic bubble.

13 minutes ago, Stefan said:

Exactly. However, you can absolutely target any enemy ship in Range 1 of the Huge ship, which is a gigantic bubble.

Assuming it is still in your arc and in range.

Oh, look. Another thing learned today.