Say I have a character on the board already equipped with all three Fate Artifacts. I then use an effect from either Gorilla Grodd or Psycho Pirate, to take a charcter from my opponents side and that character is equipped with a Fate Artifact also.(Let's say Helm of Nabu) Does the Uniqueness rule regarding them come into effect? Would I have to KO the pre-existing Helm or would I get to keep both since the second Helm was never brought into play by me?

Equipment Uniqueness is checked when you equip it to a character. if you somehow managed to steal a Fated charcter while you controled a Fated character you would be able to keep the stolen Artifacts.
but if you attempt to transfer the equipment, the ones you dont move will be put in the KO'd pile due to uniqueness.