The influence of software is only becoming an issue if you do lots of processing (FX, EQ-ing, big BPM changes and such).
Yes the soundcard in your controller makes a difference, but a 16-bit/44.1KHz (CD-quality) soundcard from a good brand can sound better than a 24-bit/96KHz one from a lesser brand. Having said that, as we are the business of providing high volume level music from highly mastered (and compressed) sources (and more often than not from lossy formats like MP3/AAC), played over club/venue/rental PA-gear, it’s my personal belief that any decent controller from any serious brand has a CD-quality or better soundcard that will be more than sufficient for the purpose.
I owned and used the MC6000mk1 for 2 1/2 years and NEVER had any reason to worry about it’s soundcard. The mk2 has indeed got a 24-bit soundcard and might (in lab situations) sound better than it’s 16-bit older brother, but I doubt there is any clubgoer that will hear the difference at 103dB in a noisy danceroom.