I'm pretty new to the whole roleplaying scene and I'm still yet to play a game, and I'm unsure about the limitations of Armour Penetrating weapons. Does the Pen score also decrease the damage reduction granted by toughness, or is it only able to ignore actual armour?

Pen does not affect toughness bonus. Pen only affects armor values.

Very few things ignore the damage reduction of Toughness bonus and everything that does explicitly says so.