Shuriken S vs R

A shortcut should be to compare 14.5x(R-type bonus) to 3x(S-type bonus applied to your max damage with upgraded shuriken). (this is counting 10 hits with 30% critical hit rate)

The long, sure way would be to calculate min and max damage for 10 hits total, 3 of which are critical (7 normal, 3 crit) for each of the 2h S-type upgrades and the 1h R-type upgrades. Basically, if it's upgraded already, just add the R-type damage to yours with the shuriken. The S-type gives an added bonus to the critical damage (at rank 1 that's 250% total damage normally, at 2h s5 that's a total of 300%)

That's essentially the simplest way to check which is better for you. Your damage is high enough that the extra critical damage from the S-Type should overpower the flat damage bonus from R-Type. I recommend Excel or OpenOffice.org Calc to keep things organized.

I'm always a bit iffy on the average damage since some mobs have rather high prot, reducing the crit rate, but at the same time ALL of the Ninja skills ignore prot for crit calculation. That being said I have an R5 Lich Crocodile Anju's Shuriken now.