The Sealed Dagger: A Ninja Guide

Subtle Blow: 0/5 or 5/5 - At level 91, you will already have +27 subtle blow from job traits. You'll only need +23 more to cap. Gear will most likely keep you capped without these merits. However, if one of your TP or WS sets aren't capped subtle blow, then Myoshu: Ichi will provide +10 and Kikoku aftermath will provide another +10. If you still need more subtle blow, putting merits in this category isn't a bad idea considering that nuking is rarely relevant anyway.

Elemental Nukes: 5/5 in two nukes for magic bursting. Choose one dark-based nuke and one light-based nuke. Try to pick two elements that are adjacent on the elemental wheel. I picked Raiton (to pair with Donar Gun) and Doton (to increase duration of wind resistance down for Silence). Suiton is also adjacent to Raiton if you prefer water over earth, though.

Sange: 0/5, 1/5, or 5/5 - I use Sange often in mid/high tier content. Each use seems to throw about 15-30 shuriken depending on how often I have to recast shadows. I prefer to pair Sange with Issekigan to minimize down time. If you don't like losing shuriken, then you can skip Sange. Few people seem to like it anyway. A mastered NIN with JSE+2 neck will already have 79% Daken. Sange makes this 100%, which is about +26% more shuriken throws during use (while this is true on average, over any 60s window that Sange could have been active, your non-Sange results will vary wildly). If you don't need Ranged Accuracy but want a slightly improved TP rate, then 1/5 is fine. If you need Ranged Accuracy, then 5/5 will provide +100. I prefer 5/5 for Omen solo since the bosses are quite evasive. If you plan to use Sange, then you should know that the Curio Moogle sells pouches of Happo Shuriken for about 19k ea and that a stack of Date Shuriken only costs 80 Domain Invasion points from Zurim in Norg. I prefer to throw Happo because I hate farming Domain Invasion.

Yonin: 0/5, 4/5, or 5/5 - Provides up to HP+250. I usually tank on NIN so I keep this 5/5. If you're fighting low-tier/low-risk content (Apex, UNM, Geas Fete, etc.) where nukes actually do something, then it would be better to 0/5 Yonin in favor of 5/5 Magic Attack. If you're just below a magic accuracy threshold for landing an enfeeble, then 5/5 Magic Accuracy would be better. If somebody else is successfully tanking, then 5/5 Innin will be your go-to.

Innin: 0/5, 4/5, or 5/5 - Must be behind enemy to gain most of its benefits. Only provides Enmity -20~-10 when not behind the enemy. My trusts can't ever seem to hold hate without a considerable head start. So Innin is useless for me when solo. In organized content where a PLD or RUN holds a boss, Innin would be better than Yonin. But for fodder enemies and fights where the monster changes its target frequently, Innin is mostly useless.

Magic Accuracy: 0/5, 4/5, or 5/5 - Provides up to +25 magic accuracy (another +15 when paired with Relic feet). Really helpful for landing enfeebles. However, I've noticed that I have just as much trouble landing enfeebles with 5/5 as I do with 0/5, so I keep this 0/5. I believe my magic accuracy set is +478/+462 magic accuracy and +17/+40 Ninjutsu skill without these merits anyway. If you're missing enfeebles, don't forget to try precasting elemental Ninjutsu to lower the enemy's magic evasion first.

Magic Attack 0/5 or 5/5 - Provides up to +20 Magic Attack (with +25% ninjutsu damage when paired with relic feet). Nuking seems to only be useful for low-tier/low-risk content like UNM, Geas Fete, and Apex mobs (which I believe take enhanced magic burst damage). Even then, it's only useful with the proper weapons equipped (check out Logical's nuking video for proper gearing tips). If you're doing actual content, then this should be 0/5. If you want to throw out 80k+ magic bursts when Futae is up on some Geas Fete or UNM, then put 5/5 in this. Additionally, this should be 5/5 to help hit Omen nuking objectives. I remember doing about 48k Futae Katon while solo with 5 trusts (no Star Sibyl) in Omen once. That would not be possible without 5/5 Magic Attack merits paired with relic feet.