If you are talking about the ninendo licensed ones then no - the 3D effect remains.
3rd Party ones shouldn't really affect it either, as long as they are not the very cheap kind, which are known to have strange effects at certain angles.
They shouldn't. As mentioned, air bubbles will be annoying if you don't put them on properly, but other than that, they don't actually take away from the effect.
I have noticed the sound quality on my 3DS is a bit lower than usual ever since putting one on, though. The screen protector I have takes up the entire top part of the 3DS, not just the screen. Not a huge difference, but it is noticeable.
I got official ones (I think) with my amazon pre-order.
I put the top one on wonky, lol.
Buying one from dx what covers the whole top screen like the yes-asia picture on page one.
I can't mess that up surely...
OT: Noticed no difference regarding 3D.
Screen's a tad darker, because of the extra layer of plastic but doesn't make a difference to my eyes.
The Hori screen protectors *the ones that cover the WHOLE upper screen *exception of speak holes* are actually not 1% "retarded" the 3DS' top screen is one solid piece. so why get a little cover that only covers up the middle spot (the screen) when you can protect the whole upper screen from ugly scratches so when a next model 3ds comes out you can trade it in for the most amount of money you can get or sell it on craigslist for damn near brand knew? the better you keep your shit the better you're off.