I think the 5.5 includes the virus and the 5.0 doesn't.
think of it as a bonus.
Actually, there were some revisions to the hardware specs, I read that somewhere when I ordered the shuffle for my wife, but, it was one of the mac enthusiast sites that went over some of the changes. I believe the 5.5 had longer battery life and a brighter screen. 5.5 has gapless playback (which the shuffle has) and a 5.0 model can be updated to 5.5 with firmware.
I found some vague mentions at fatwallet and macrumors about the differences and the above is a summation.