What the f**k is multithreaded?!
Short explanation (regarding why that is better for N3DS):
A multithreaded program executes commands in multiple threads in parallel.
These threads of commands can be executed by independent cores (or processors).
So, if you have multiple cores (like the N3DS), making a program that is multithreaded means the additional cores are used and you can achieve better performance (speed, framerate, whatever).
Long explanation:
Multithreaded code actually does not need multiple cores to execute. Parallel execution can be simulated by e.g. time-slicing, where one processor executes one thread for a given time, then the next thread, and so on.
Multithreading exists since long ago, and gave a sensation of parallel task execution since the old times where consumer computers had normally only one single core CPU.
In those days multithreading did not help to gain performance, but to improve usability of the computer.
Think of old MS Windows (3.xx, 95, 98) or well, all kind of old multitasking OS and PCs.
Anyway, today with multiple cores and multiple processors, it results on improved performance when used correctly.