NeoPixels' timing requirements are pretty tight - not necessarily high frequency but high accuracy, for at least certain parts of the serial pulse train. To achieve that, I believe the (Adafruit) NeoPixel library takes over one of the timers during the transmission and turns off interrupts for at least some of the time. That will have a negative impact on any background processes. Read through the NeoPixel library code; it should be clear.
However, while researching my answer (so as to not embarrass myself too badly!), I found this article at josh.com that describes driving NeoPixels with a much lower impact and goes on to demonstrate his technique with a video of a 1000 NeoPixel string(!) driven at 30 FPS by an old, apparently Atmega 168-based, Duemilanove.