I know it doesn't make a lot of sense that emulators have been developed that can run just about any N64 game or any PSX game at full speed while the same cannot be said about DS games (which have roughly the same caliber as games from the aforementioned systems), but unfortunately this IS the case, and it's just a fact of life that we have to accept for now.
We've all taken for granted that we can play just about any previous-gen system we want at full speed with no issues whatsoever. DS emulation will eventually follow suit, but right now, what it comes down to is that different emulators play different games with differing performance levels.
The game you just listed, Phantom Hourglass, is relatively new and uses 3D elements, and so it's not too surprising that it can't be run by any emulator at full speed yet. But of course, there ARE games out there for the DS that can be played at (relative) full speed and full capacity on at least one emulator out there. The list of these games, as well as the performance levels, changes all the time--basically, whenever a new version of an emulator (or a new emulator altogether) comes out.
So, do what I do: Every single day I check back to these forums to see if there's an announcement that a new version of an emulator (or a new emulator altogether) has just been released. I actually find this waiting process to be kind of fun; basically, to see technology in the making, and to see these programs that will enrich people's lives being refined over and over again. Like I said, it's technology in the making, and it definitely helps that I find programming fun and interesting in the first place. Of course, I have a LOOOOOOOOOOOOONG way to go before I'm even close to the level of the people who develop these emulators, but hopefully, one day, I'll get there, and maybe by that time I'll be helping to create--as a personal project, separate from my actual career (which will also be programming-related)--emulators.