I had read a theory that says the knot represents the mystery of the ship. One of the sailors throws it at Delano in a half-in-code, half-metaphorical plea for help ("Undo it, cut it, quick"), telling him to put the pieces together and figure out the truth about the ship. He fails utterly, just like he fails to untie the knot when a Black man comes and immediately takes it away from him.
Melville isn't racist, he is calling out America for its racism, back before the civil war. Delano is so racist that he doesn't even know it. Everything he does and thinks as a "leader" is drenched in racism. He was duped by Babo because he couldn't fathom that a black person could lead. The story is written in Delano's perspective, and that's the point... to silence the black perspective, because it is silenced in much of the world (still unfortunately).
