KH underperformed, I thought the hype around it was pretty big, so I was a bit bullish on how it'd sell. I wouldn't call it a bomba, but I think SE did expect more. If anything the blame shouldn't be on the 3DS, its the next Japan console, it being a kiddy console or that only Nintendo games sell on Nintendo consoles excuse doesn't fly anymore. Proper core third party support is on it, and everyone knows. We'll see how its legs go, if it ends up around 500k, I doubt SE would think much about it, besides its how it sells worldwide that matters more.
Userbase, bad reputation from previous entries and franchise fatigue would also have an effect, its not like Kingdom hearts isn't mainstream enough for the userbase to not count and its not exactly popular enough to be a system seller to every fan. Hell, One piece gave the PS3 a bigger boost than KH did to the 3DS.
KI on the other hand had a nice drop, I'm really hoping it gains a good pair of legs.