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For the first question, No. the only thing Shroud and hexproof look for is "target" and once something is on the creature, it is no longer targeting, but a part of the creature. The enchantment Pacifism would not be destroyed if the creature gained shroud or hexproof, but it could no longer be enchanted by something new.
For the second question, yes, the Pacifism would be destroyed since protection does the following. 1) prevents damage from the chosen color.2) gives inability of the colored creatures to block the protected color and 3) all enchntments of the chosen color are put into the graveyard as a state based effect.
502.7c - A permanent with protection can't be enchanted by Auras that have the stated quality. Such Auras attached to the permanent with protection will be put into their owners' graveyards as a state-based effect. (See rule 420, "State-Based Effects.")