Im just going to take a wild guess and say its because developing SMT games for the ds/3ds is not expensive at all, and also due to the fact that they do not have to be graphic intense because people would be like "Well it is on the ds/3ds so the graphics will only be so good." With such a low budget for these games, you do not have to sell as high number of copies of the game, unlike if you make a very high budget console game. However, I think that with games like Persona 5, people expect it to be on a console like Ps3. What comes with that is expectations that the graphics and other areas are very high quality, kind of like Catherine. Much bigger budget, and what comes with bigger budgets is that you have to sell more copies of the game to profit. I dont know if you will understand that, Im kind of bad when it comes to explaining some stuff xD

If anything the Persona stated for 3DS will probably be a port of the early ones, which are very similar to the SMT games that are on DS/3DS anyway.

Atlus originally stated already that the game is currently being developed for PS3. They didn't say exclusively or anything, just that it was def there for the time being. That was a while ago. I don't think that has changed except it might go cross gen with PS4/Vita.

The SMT games that are on DS/3DS must be unimaginably cheap to make (they look it) so any amount of sales will be positive for them. Not to say if they put more effort into them like the Persona series it wouldn't do even better.. Just don't think the 3DS of all systems can handle tech wise what most fans are wanting in the next game.