I do both, depending on the track I'm making. Most of the time, I don't manipulate the pitch/time of the sample at all. I chop irregularly on purpose and often have noise/artifacts in the chops that I use in my tracks using a "masking" technique, where I mask the noise so it provides a syncopation to the beat. The irregular chops (not chopped on any beat - often several beats in one chop) allow me to flip the samples in different bpm tempos. Also, the "zero crossing" you mention may result in noise or pops - usually if your chop ends or begins with the transient above or below the zero line.