No I don't think Nintendo is that stupid to ignore the huge install base on the old 3DS for the time being however looking into the future the will be many games that are going to be New 3DS enhanced that look graphically better on the New 3DS with extra features and no hit on performance when 3D is turned on (thanks to the GPU core speed on the New 3DS being double that of the old 3DS, which I believe is true just not yet confirmed).
Think of it like this, the old 3DS will be like what a 2DS is right now once developers start making New 3DS enhanced games that not only looks better in 2D but will also have better effects in 3D while retaining the same performance with 3D turned on. Meanwhile these New 3DS enhanced games on the old 3DS will not look as good and will probably take a performance hit with the 3D turned on, it's not like a lot of old 3DS users use the 3D anyways since it's nowhere as good as the face tracking 3D from any angle on the New 3DS. Which in turn essentially tuns the old 3DS into a 2DS because not many old 3DS users will be turning on the 3D due to the weird angle it needs to be held at for 3D to work and the performance hit on newer games that are New 3DS enhanced.
tl;dr
3DS -> 2DS because 3D not worth it with crappy viewing angle
N3DS -> new 3DS because better insides and 3D worth it because revised viewing angle.