Let me try and explain my question a bit better.
If you don't reject frequencies above the Nyquist limit, you get aliasing distortion. Therefore, in the beginning of digital audio they used filters to reject these frequencies. Typically these filters were very steep in slope (90 db/octave or so). "Brickwall" I think was the term used. As most of you know, very steep filters have a noticeable effect on sound... they introduce phase distortion; the steeper the filter, the greater the distortion. 90 db/octave that is 100% rejection at 22 kHz can distort frequencies all the way to 10 kHz.
So, you have a choice then - either use a more gentle filter (~40 db/octave) and accept some aliasing, or use a steep filter and accept phase distortion.
Which brings us to modern digital audio. AFAIK, almost all decent A/D converters "oversample" to get around this problem. In context of an ADC, this means (IIRC) that they are actually sampling at a higher rate (instead of just interpolating more samples, as in the case of a DAC). In this way, the filter requirement is shifted to a higher frequency, just as I was talking about earlier. The ADC might actually generate 88.2k samples/sec, but only use 44.1, if it uses 2X 1-bit SD oversampling (again, IIRC).
So, if your "good" ADC is using oversampling anyway instead of an antialiasing filter that will cause problems somewhere, why not just keep the 88.2k samples/sec instead of discarding them at the ADC?
I'm assuming now that if dropping every other bit (or three out of four, in the case of 4X oversampling) doesn't cause a problem (or at least, not as big as the one it solves, or it wouldn't be used in high end gear), then it shouldn't cause a problem when you downsample back to your target format, so long as you used an even multiple sampling rate to begin with.
I also wonder what effect this has during effects processing. Are there any practical drawbacks? Do plugins not like odd sampling rates, like 88.2, or can they cope with most anything as far as sampling goes? I know some plugins don't like 24 bit resolution (or 22, or 20 or whatever), but I don't know if they are sample particular.
Bottom line - maybe it doesn't make the sound any better to keep sampling rates high throught your processing chain. Perhaps it's only the resolution that matters, and the sampling rate is not important once you actually have the sample (and have avoided aliasing, and phase distortion, etc.). i.e., perhaps it sounds the same to downsample all of your tracks from 88.2 to 44.1 before effects and mixing as it does to downsample the final mix. I don't know... I never got that deep into digital audio theory. I'll probably find out though.
However, I don't see how it could sound worse to keep 88.2 throughout your processing and mixing. After all, your ADC, if it is decent, is probably creating those samples anyway. If it is capable of retaining them in the ouput, why not? The only certain downside I see is file size.
Any thoughts on this?