I wanted to make a fast test to see it myself.
To begin with,
the info of skill implied in damages comes from official site :
Update from 07 decembre 2010, Battle related section...
Quote:
Elemental ninjutsu damage now increases based on ninjutsu skill.
*Effect active only when main job is set to NIN
I tested with Constant mobs
Wild bunnies from E ronf, one shot 100% , constant day, weather, gears, skill capped and merited etc...)
I only changed head gear :
1/Empty 2/INT 3/Koga+5% 4/Hatsuburi+1=Ninjutsu+5
According to numbers :
ICHI had no benefit from Ninjutsus Skill to damages.
NI had no benefit from Ninjutsus Skill to damages.
SAN had a benefit from ninjutsu skill.
(something like +0.3% per +1 skill?)
I'll test more, to confirm or not, with a larger skill difference.
Naked with Koga tekko, then +30 skill from gears (head, neck, boots, earrings)