Audio Bit Depth/Sampling Rates, How to choose the best one for your task at hand. Options

Ok, so there are dozens of cards and systems out there that will allow you to record in 24 bits and 96 khz. But as far as I can understand, unless you are creating/recording all your samples yourself, ultimately you will be faced with having to work in the lowest common denominator of all your sound sources.
For example, I sample extensively from CDs and there are dozens of CDs being produced for this purpose, all/most of which store audio in the standard CD format of 16/44.1. Moving files to higher sampling rate environments causes changes in playback speed...how do you get around this?
Do you pitch shift everything and make it right--sounds like a lot of work. Or do you just live with it and compose in 16/44.1. If that's the case, then if your sources are CDs, etc, what purpose do DA cards serve? None would be my answer, but I don't have a lot of experience in this regard--yet. So I put the question to all you experts out there...how do you get around the problem of the lowest common denominator?