First of all, let’s assume that you don’t want to use an NDS flash card to play music.
Then, yes, the audio and video must be placed in the SD card and completed through the music player or video player that comes with the 3DS. Note that the video player will only appear if the machine is upgraded to 3.0 system.
There are system folders in the SD card, but there are very few. If you don’t take pictures or download things, the 2G space will basically remain untouched.
In addition, there are now dedicated 3D video downloads for 3DS online. Each file is currently limited to 10 minutes, so if you want to watch a movie, you have to download a bunch of segments. Of course, you need to use a card reader to read the SD card.