peter,
theoretically 'bits is bits' whether they come from a cd or a hdd however as jitter is primarily an issue between transport and dac (hence naims insistence on keeping the distance between the two to a minimum) the quality of this interface and the clock controlling things is important.
the squeezebox has a pretty good reputation for jitter performance but as i posted a few posts back there are differences in the quality of the output differeing between flac and mp3 playback leaving room for improvement.
all that said - it's really splitting hairs and can pretty much be ignored.
cheers
julian