Well if the AI is smart enough to get shield equipped units stop and adjust their facing when a missile unit is near it would cut down on casualties. If the enemy troops were just stationary targets just trying to weather the barrage, this might work, but in other cases I suspect this would be hard to code and dependent on other factors, ie you wouldn't want the AI to stop if it was a cavalry unit charging your ranged units.

Anyway we've had some previous discussions on this regarding archers, lowering their attack and increasing cost/upkeep:
https://forums.totalwar.org/vb/showthread.php?t=40765
and a more general discussion:
https://forums.totalwar.org/vb/showthread.php?t=39757

as well as a mod to nerf attack values for missile units:
http://www.twcenter.net/downloads/db/?mod=210
where Rhodians/Balearics get 7 for Missile attack and sounds more reasonable to me.