Take off any crit-increasing gear/titles, stamina potion poison yourself down to 0 will, then look at your crit (try to get it slightly less than 30%) and go fight monsters that have over half your crit rate in protection. You shouldn't be able to crit on them at all normally, so if a skill does crit then that skill ignores protection for crit calculation.
I was able to get myself down to 28.2% to 29.7% crit with this, and testing the skills on the first-room enemies in The Other Alchemists (all with 19% or above crit meaning -38% crit if protection is a factor and assuming their protection on the wiki is correct), the results for which skills were able to crit through protection or not is...
Shuriken Mastery: No
Shuriken Charge: Yes
Shadow Cloak: Yes
Explosive Kunai: Yes
Kunai Storm: Yes
Smokescreen: N/A
Shadow Bind: N/A
Sakura Abyss: Yes
To make sure things were correct, after testing all of the skills I finished off the next wave with nothing but normal attacks,
and didn't get a single crit with a normal attack the entire time I was in that mission.
So it looks like
ALL the damage-dealing ninja skills ignore protection for crit chance (minus the weapon mastery of course). That explains them nerfing red upgrades on shurikens (420 damage needed to bypass blue).
EDIT: A screenshot from when I was testing, right after Shadow Cloak crit.
[Image: http://s29.postimg.org/c6r8zf5on/mabinogi_2014_07_24_001.jpg]