It appears some ranged attacks already affect morale, i took this from descr_area_effects.xml, you could perhaps test this by adding their names to arrows in descr_projectile.txt.
Code:
<area_effect>
<name>ae_cow_carcass</name>
<type>nausea</type>
<ground_effect>cow_impact_ground_set</ground_effect>
<floating_effect>cow_impact_wall_set</floating_effect>
<radius>10.0</radius>
<duration>300</duration>
<banner_colour>
<red>0</red>
<green>255</green>
<blue>0</blue>
</banner_colour>
<morale_effect>-5</morale_effect>
<morale_max>16</morale_max>
</area_effect>
<area_effect>
<name>ae_greek_fire_fear</name>
<type>nausea</type>
<radius>5.0</radius>
<duration>30</duration>
<banner_colour>
<red>255</red>
<green>0</green>
<blue>0</blue>
</banner_colour>
<morale_effect>-10</morale_effect>
<morale_max>16</morale_max>
</area_effect>