Does ion damage penetrate shields?
No, Ion Damage is handled as normal, plus an Ion token

This is addressed in the core rules on page 16 under the heading "Suffering Damage":


  When a ship suffers damage or critical damage, it suffers them one at a time following these steps. ...
  1. Reduce Shields: If there are any shield tokens remaining on the ship's card, remove one of the tokens and skip Step 2. ...


(Emphasis theirs)

The rules for receiving damage are separate from the rules for dealing damage, so unless the card specifically states that it bypasses shields, the targeted ship would receive the 1 point of damage following the normal rules.