I think a history of singing spirituals isn't long enough (since the 1950s) to have estalished Japanese versions. A lot of choirs and singers alike haven't sung them in Japanese; I can't sing any spiritual in Japanese. Hara's translation appeared first in that hymnal in 1967, and is not widely known (the spiritual itsef is well known, though). Furthermore, "Deep River" isn't contained in Sanbika 21 (The Hymnal 21), published in 1997 (Hara is a member of the editorial committee). From where Endo's epigraph comes, I don't know. It doesn't seem to be a singable version.
~Masato