2d RPG with female ninja on the DS?
The Izuna games maybe though I don't particularly recall her using a chain weapon (might have been an option as it did lean into "ninja" weapons there), though I did not do the most with the sequel. Not to mention these were roguelikes/dungeon crawlers, though I can see someone lumping it in with RPG (you have characters/witty dialogue, and fighting is not so very different to many other games that would be called RPG).
You can fight as a female ninja in The Legend of Kage 2, and she does use a chain weapon (though many games do lump their kunoichi with such things), however that is straight up side view action game.
After that though it gets difficult (you said no to ninja gaiden, ninja reflex is a minigame thing as is Ninja Captains and ninjatown is anything but that description, though a pretty good game). Don't know if one was left in Japan or something. Don't think it would have been any of the Naruto games (though being anime games I mostly skipped over those, scan of some of the screens says no though).
Have not done the most with the oddities of the 3ds library in case you misremembered that and I don't recall anything from the GBA library either.