You deal 25% more damage with silenced weapons. Stealth is also increased in shadows to 10% less visibility, equivalent to half the effect per rank of the Sneak perk.
As it is a percentage damage bonus that applies to the weapon's damage all the time, not just when making sneak attacks, the order in which it is acquired has no effect on the Cloak & Dagger > Ninja 3 > Mister Sandman 3 damage multiplier calculation. It can be earned at any time with no change to the final damage bonuses.
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