Sure, most of the viewers won't know Japanese, but I don't think that's a good reason to make "kekkai" look like a different word. I don't see any issue with just leaving it as "shinobi kekkai" (probably preferred) or "shinobi barrier". If necessary, a single liner note would be fine on its first use. "Zaibatsu" was left alone in the subtitles without any sort of given or implied meaning. If some Japanese words will be left in, then a redundancy like "kekkai barrier" just seems unnecessary.