Does the other section count as a different target?
Can you fire cluster missiles' bonus attack at a different section of a huge ship?
No. They tossed out the 1.0 Epic separate "sections" in streamlining for the conversion to 2.0 Huge ships. A huge ship is a single target.
Yeah, the 1E Huge ships, with 2 sections and a damage deck for each section was kind of a pain in the butt. Epic play in general very badly needed streamlining.