To remain protected from exposure to the potential corruption of magic, Assassins must defeat their sorcerous opponents without actually using spells themselves. To this end, they have mastered the clandestine talents, as well as the arts of obfuscation, and honed their latent psychic abilities to develop the Shadow Disciplines. These skills represent the end result of generations of strict mental conditioning and intensive stealth training.
This set of skills adds to the mystery and power of the Assassin. The Shadow Disciplines don't make the attacks, they make the attacks better. They don't hide the Assassin, they make her harder to see. They can also cause poison damage and summon a Shadow Warrior to fight at the Assassin's side. In short, the Shadow Disciplines are a set of very important skills that augment the Assassin's other skill sets, while still providing a great set of unique and devastating abilities.
The "active" skills like Burst of Speed, Fade, Cloak of Shadows, Shadow Warrior, Shadow Master and Venom can still retain their effects when you swap weapons. Therefore, if your secondary set has better bonuses to Shadow Disciplines skills, you can activate the skills with this set and then swap back to your primary set to be used for combat.