If I attack a CR90 or Raider with plasma torpedoes, can it remove a shield from either section? If so, who decides which section the extra shield damage comes from?

No. You target a section of a huge ship with two ship cards. After the atack is resolves against the targted section you remove another shield from that section if it has shields left.

In the EPIC rules, if damaged is assigned to a non specific section or both sections, it gets assigned to one at the opponents choice.

(At work and can't copy/paste relevant section)

example:

Seismic charge goes off and hits both sections. Opponent picks which section gets that 1 damage (but not both).

Read splash cards carefully. If they state that a "ship" suffers one damage, then you can't have an EPIC ship have both sections hit (that would be a ship taking 2 damage).

This is true. But plasma torpedoes does not deal unspecified damage.
They remove a shield token from the defender. And during an attack on a section of a huge ship, that section is the defender.