Citizens of the south suffered food shortages during the civil war because?

Well, think about it: if the boys are off to war, who's tending the farm? Actually, a more importation reason is distribution. War is confusion, and normal traffic is interrupted, sometimes by enemy action, sometimes just by people running around with conflicting objectives. As Union forces advanced into Southern territory, they deliberately confiscated the crops to feed their own troops or else destroyed it to starve the rebels into surrender.