I disagree with this theory. While my knowledge of the Japanese language is crappy (re: I know only what I've gleaned from anime), none of the NIN job characters fit into this. Oboro translates to "dim," and while this might be ninja-themed ("Dim Moonrise," making it easier to be sneaky) the names don't really have anything to do with each other. Tsubame translates to "swallow," as in the bird (Karasu even taunts her with this, "Look, swallow, I know you love me."). Karasu similarly translates to "crow," which has nothing to do with his supposed surname (crows don't have red beaks).
Even Yugiri Mistwalker I find suspect. I don't know what "Yu" can translate to, but if "Mist" were in her first name it would probably be "Kiri-" something. (Kyoko Kirigiri, of Danganronpa, has a last name that translates literally to "fog cutter.")
But again, my knowledge of Japanese is cursory at best, and there is the high likelihood they're all using pseudonyms because they're ninja.
Not ALL the refus are ninja, but a fair number of them are; you interact with them on occasion after 2.2, and Yugiri uses them as spies and contacts throughout Eorzea for the Scions.