I understand the difference between AR and VR from the user's perspective; just not the opponent's. As far as I understand it, any user jacking into a node--whether through AR or VR--shows up as an icon to everyone else in the node (SR4a p. 224, "When you log on to a node, your icon appears there").
I'm not trying to reverse what's happened to Rybka--I'm willing to accept that these guys are serious enough that they'll assume anyone hacking into their system is probably in full VR, and thus respond with black IC immediately (though in that case, we're REALLY not getting paid enough on this job!)--I'm more wondering for the general purpose.