Thrown weapons is a ranged weapon skill, and is totally separate from the blade skill, which applies only to melée. A thrown weapon is equipped in the slot at your character's shoulder like all other ranged weapons such as bows; a melée weapon is equipped in the character's hand. So, a throwing dagger is completely different from a dagger. Because it is a throwing weapon, you cannot equip it in a character's hand, and likewise, you cannot equip an ordinary dagger in your character's shoulder slot. The same applies to an axe (must go in the hand) and a throwing axe (must go in the shoulder slot).
Therefore, the second attack with daggers in the GM Thrown Weapons description applies only to throwing daggers.