First of all, if you will have any chance at all to hear any difference, that will depend on your HU. Not all HUs support uncompressed or lossless formats. You will have to check your manual for this, and pay extra attention to supported formats, and not the least, supported bitrates for each format. I've heard some HUs are supposed to be able to play lossless through the iPod with a special cable.
And regarding the sonic quality from playing directly from an iPod, many claim that they experience better sound when playing from a hard drive, than from their CD player (mostly in the home Hi-Fi crowd).
Non of the above is unfortunately from my own experience, but what I've heard during my efforts to find a HU that will have inboard or outboard processing and that will let my play lossless or uncompressed music from an iPod. That is, it's all hearsay, or regarding the first section, taken from various manuals.