The only point going beyond 44.1Khz sample rate is when you record something. Essentially it affects the quality of recorded material, because you have more sample positions per second. When recording something from analog (microphone, line ins, all that), use the highest sampling rate possible with 24bit depth. Recording something inside your daw, like bouncing a track to wav, it shouldn't have a notable difference, but there's certainly no harm in using a higher sampling rate. The only problem will arise with using 44.1 samples in a 48Khz project, because the DAW will have to resample all the sounds and that might create small amounts of noise. not 100% about that last part, but the noise levels shouldn't be a problem on modern daws, depending a little on the sample interpolation method used.
In short - It doesnt really affect much anything when you work ITB.