Well, only "FPS" I can remember playing on DS was Metroid Prime and it was just appalling to play. Some of the worst controls I have ever encountered in a game... like ever.
3DS may have an analogue stick, but it only has one, and I can remember playing FPS titles on my PSP like that and the experience was... well... not pleasant to say the least.
On 3DS, when I try to imagine camera controls for 3D games, all I can think of is Kid Icarus... and that shit was just the worst. Poster child for why touch screens are the worst way to control a camera in a 3D title.
That second analogue add on might make FPS' playable on it though, but without a test case of some sort it's mere speculation at this point.
Bro-fist.
Killzone Mercenary is really in a class all it's own on the handheld FPS front. Amazing game.