To my knowledge the only way to get a exotic Cypher is doing ours quest every weekend. I hope you plan on putting them in some kinda content if it's the new cost of focusing new exotics.
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I think the season pass gives out a couple but after that yeah the only source is from the weekly quest Xûr has. I think (I haven't run the quest cause I don't have a reason to get ciphers) you can run it on each character giving you three a week but I could be wrong.