I say, go ahead and develop DS emulation on the 3DS, there are plenty of people that want it. Personally though, I'm going to stick with my flashcard regardless, and this is for a few reasons:
1. My 3DS is fully self contained meaning that I have no reason to ever even remove the one physical cartridge in the 3DS (as all my 3DS games are now digital copies). As such, to make my 3DS feel complete, I'd like to have one cartridge always in there, my DS flashcard seems like a no brainer to be that cartridge in this regard. (I do still keep a copy of Cubic Ninja around though, just in case I do ever need to do some debugging or whatever, but very rarely do I need to remove the flashcard to put that in).
2. I have a lot of DS roms, I also have a lot of 3DS titles. Consequently my micro sd card in the 3DS itself is nearly full (its 128GB), and that's with no DS rims on that micro sd card. Fortunately the flashcards allow us to use another micro sd card specifically for DS games (mine is 32GB and that too is nearly full).
3. Beyond all that, I'm not convinced that DS emulation on the 3DS will ever get nearly as fluid as just using a flashcard.
Still, I think its nice to have options, especially since I know there are a lot of people that had been wanting DS emulation for a long time.