Azizi,

My ~guess~ as to why they would have used "Haul Away Joe" in Roots:

It was set pre-1776. However, we don't have any evidence to exactly what chanteys might have been sung prior to the 19th century. We know there was some kind of chanteying, but it is all conjecture which of the songs (i.e. the ones known to us today) would have been used, if at all. One of the popular ones to conjecture existed back then is "Haul on the Bowline." That one has similarities to "Haul Away Joe." So my guess is that, pressed to speculate on what may have existed, they chose those two.

Gibb