To get usable results (but not even with this 100% on the most games) you need to run the emu completely on bare metal without anything other running like the os and you need anything the 3DS has (all 3 ARM cores, GPU, DSP). But as already metioned, the 3 ARM cores don't make it better, if you are bad at multicore programming. The architecture difference between ARM11 and 9 makes it even harder to get this running and optimised.
The thing with programming for muticore systems is a lot like carrying buckets of water.
Imagine that there's one guy
(CPU core) carring two buckets of water
(instructions) from a well
(binary) to a tub
(execution) versus two guys carrying one bucket of water each performing the same task from two separate wells. Everything is fine and dandy and the same amount of water is being transported... as long as the two guys aren't bumping into each other along the way or queuing at the tub to dump their bucket
(desynchronization, one core idling because the next operation requires data that hasn't been processed by the other core yet) and the wells aren't drying up as they're doing it
(Idling when the tasks in one thread are substantially more demanding than the tasks in the other thread, so one core is running at 100% stress and the other is having a nap).
Needless to say, achieving 100% efficiency is nigh-impossible with this kind of a setup when you don't have overhead processing power to waste, and unfortunately, the 3DS doesn't have that. It would require a lot of optimization to squeeze out every last bit of processing power to make this thing work properly.
Now, don't get me wrong - I'm not dissing multicore! Running multiple threads on multiple cores at the same time is extremely beneficial in contemporary applications... not so much in older applications that are merely being interpreted or recompiled live during emulation. A multicore setup is actually highly desired when emulating platforms that are multicore/multi CPU themselves, since you can emulate each core or CPU on a separate thread and a separate core, but again, this more often than not requires overhead processing power that you
can waste while idling.
There are ways to go around these problems, yes, but they're rather complex and take time to develop and optimize, so a
"playable" N64 emulator on the 3DS in the nearby future will remain within the realm of day dreaming for a couple years.