There is no extra moral penalty on the enemy for where your shooting from, but the mere presence of a squad at their rear or flank has a moral penalty. It negates the shield, as said by Maeda, but if your archers are close (which is likely) and on even terrain then only the front rank of archers will fire, meaning less arrows and therfore less deaths.

Flanking with ranged units works far better with crossbow/arbalesters or mounted ranged. THe former because of the flat trajectory and sheer killing power, plus you don't shoot your own troops in the back, the latter because of speed and mobility.