YEah and in that Secret Charecter Story battle where you get the Genji armor you can also get the Masamune by stealing it from a Samurai.Different battle in. You get the Genji Armor as a trophy from *spoilers* the Aliste battle. You steal the Masamune from one of Bremondt's girlies inside Lionel, the battle right after the Aliste battle. This is a Beowulf and Reis based sidequest. *end spoilers*
You only need ONE debuff to get ninjas to use throw. Immobilize. They will sit there and chuck weapons at you like theres no tomorrow Or Stone. In Midlight's Deep, I trap the ninja on a specific spot, surrounded by pit squares and my allies turned into statues. You don't have to reinflict Immobilize, the enemy doesn't waste time moving, the designated "catcher" is the only one who is in range of the trapped ninja (unless the ninja has Move + X), and the "control" character who manages the situation and is your safety net can repeatedly put themselves to sleep by stepping on the trap.
However they need to be a correct level, and have only the skills that will make them choose throwing katana's over other objects... or you need to manipulate your hp, so them throwing katana's would be the one that kills you if it gets by.I didn't find it that big of a deal. The biggest thing is you can't even tell if they can throw katana unless they are throwing them at you. In order to be sure, you have to let them hit you, which can be a pain. Then you have to manage their levels or exp, requiring a thief (Balthier rules for this) or a Mind Flayer + Level Blast.
As far as having to manipulate things to have them throw katana at you, I'd like to point out that they actually don't always choose the ability that will do the most damage. The many times I've farmed catchables, the trapped ninja would choose different throwables, sometimes selecting shuriken or bombs even when the target was at max HP. I believe you see more of a tendency towards the rare throws when the "catcher" has high max HP and is at or near full. When you are at lower HP, the enemy will often throw weaker throwables at you. Also, some specific enemies with specific throwables would throw what I wanted almost all the time. Comapre that to Nagraroks; it can be frustrating waiting for the ninja to decide to throw them at you since they do so little damage.
---I know, I know. Everything I post is tl;dr---