I presume you're suggesting the Rogue is attacking an Ethereal fighter.
The answer is No, they don't ignore the armor and/or shield.
First, the Ghost Touch weapon can't attack to the Ethereal plane, so they can't make the attack in the first place.
Second, if they're using a Force effect weapon of some sort, so they can make that attack across the planes, the protective gear is as "solid" to the weapon as it's wearer.
Slightly off topic: I once pulled a dirty trick, as a DM. I had an entrance way "blocked" by a Wall of Stone that existed on the Ethereal Plane. Most people/creatures could neither see nor feel this barrier, and could walk through without a problem. But people with Mage Armor, Shield spells or Bracers of Armor, which are Force effects (and thus cross the planes), couldn't pass that doorway. They couldn't see the reason, they just ran into the stone wall that wasn't there for anyone else.
Took them some time to figure that one out.
