Use a lower brightness setting like 2 or 3 and don't play in a completely dark room or near a window where it's too bright, what kind of lightning conditions there are where you play have a big impact on whether you will experience ghosting or not, experiment with those things until you get rid of it and remember that there are different kinds of light too. Also lowering the 3D setting helps a little.
Ghosting happens when light escapes through the parallax barrier that occurs when your 3DS is displaying images where there is a big difference between blacks and whites.
For example a white character standing in front of a black background can cause ghosting while a blue character in front of a black background won't give you ghosting at all.
It's a really rare occurrence to experience ghosting when playing in normal lightning conditions and it really depends on the software, LoZ
oT didn't have any at all but I've seen it in eShop demo's before.
Some games are optimized against ghosting like Kid Icarus and completely gets rid of it thanks to in game lightning methods.