When the game asks what kind of 3DS it's running on Citra will claim "New 3DS".
Citra will not be faster or anything using this option. The opposite is the case: This means the game might try to use better graphics etc. which will make Citra slower.
Some games might depend on running on a "New 3DS". However, for now we don't support all "New 3DS" features either so you should keep this option disabled unless you are a developer.