I have and continue to run into that issue. On a personal as the GM stance, plant type creatures who are not humanoid should indeed never be able to have armor profs. On the other hand any humanoid plant type creature should be able to benefit from armor as per the character class they are using. That is just my personal feeling on the matter. As I think the RAW are referring to plant type creature that are not PC's and are using the plant creature type as their advancement template, rather than a class. I would post this to the Ask (insert Paizo employee such as Mark S.) threads for a more (but not absolutely) official answer.
Yes they can wear armour and gain proficiency with it. Ghoran have no racial HD and are defined by their class levels, so will automatically gain the armour proficiencies of their chosen class, same as any standard PC race.
Plants with racial HD don't automatically gain armour proficiency, but there is nothing preventing a plant gaining proficiency. Even without proficiency there is nothing stopping a plant wearing armour. It will suffer penalties and the armour will be more expensive (as per the armour for unusual creatures table).
Proficiencies are additive.
If your race gives you no proficiencies but your class gives you light/medium armor and simple weapons then you are proficient in light/medium armor and simple weapons.
If your race gives you martial weapon proficiency somehow but your class only gives you simple then you have both simple and martial weapon proficiencies.