I've not heard a difference between wired v. wireless, though I've not done any official head-to-head comps - just casual listening set up one way, and then more casually listening at a later date set up the other way.
FWIW, at first I had trouble running 24/48 over my Linksys Wireless-G access point (WAP54g v.2). My WAP was 5 thick, old-construction walls away from the SB3, and I had trouble with skipping. I also had trouble with reliable wireless for PC in the same room. Not so much a squeezebox issue as a wireless issue, it turns out. I applied a hacked firmware to my access point to increase it's broadcast strength, and no problems since. Couldn't be happier. I'm totally media-free now in my listening: PC > DAC > Audio Experiences Symphony / McCormack DNA-1 > VSA VR-1s in the office, PC > router > wireless > SB3 digi-out > STR-DA3000ES > VR-1 for living room, and iAudio M3 for portable audio. Love it across the board.