The 3DS has a lot more JRPGs than Vita. If you want to count the Playstation Store and PSP games then you also have to count DS titles for the 3DS and... 3DS wins again.
It really doesn't make sense for NIS to ignore the console. The only reason I can see must be a commercial agreement.
Please let's take a look at a rpg list on 3DS and compare it to Vita.
On the 3DS side I only see games that are from Nintendo (Mario & Luigi, Pokemon, Yo-kai Watch, Xenoblade), come from DS and thus proven to work on a weak system (Etrian Odyssey, Devil Survivor) or that sell regardless of anything (Monster Hunter, Final Fantasy).
While on the Vita side, just look
I only see games that always have been on more powerful systems because they need it to fit all the content and look good to do justice to the waifus.
You can do a comparison with Conception 2 that came out on both, after seeing the Vita version you'll start puking only of thinking about the 3DS version.
As an example a game that could have benefited from being on Vita is Lord of Magna. The game uses prerendered sprites instead of real 3d models because the screen fills with units that the poor 3DS won't support it. I'm enjoying it, but I think I could enjoy it more if was a Vita title.
So, this:
Probably because the 3DS is a potato compared to the vita, which greatly limits what they could do on it versus the vita.
Only the Vita has enough muscle to make games look good (I'm not going to include smartphones here as they are not a gaming platform).
And don't take me wrong. I'm not one of those elitists that think graphics are everything but if you are gonna do something, you better do it well.