We only have half of his skillbooks now (we are missing his other 2 chases and standard attack) as well as skill mutations later on. Later on we should be able to modify skills the same way purification works- we get a random skillset from all available ones. Current breakthrough will set minimum, so lets take an example of his mystery: 0, +1, +2, y, y+1, y+2- if you make kirin +2 now, later on u wont get lower than that during dice roll.

If you can utilize his mystery during ranked/gnw and actually get that paralyze off, its worth to fully break him. It also increases mystery dmg by small margin (tested kirin +1 and +2 on a dummy, had about 10k hit with first and 10.5-11k with +2). I have all his current upgrades, and from my experience, if you cant get mystery to hit, theres no difference since we dont have dmg skillbreaks yet. However later on, with good chases he really starts to hit hard and might be a strong ninja, so current farming will profit in a long run. As for fragments, there are other ninjas that you can buy in redemption market that will contribute towards fragment refining, so saving his frags wont hit your refining that much. It's up to you, you need to decide if you want immediate points and few more scrolls/irukas/9tail frags or small power boost and easier skill draft later on. That is, if you will use him, if not then go for refining with no hesitation.