When I do it, you can be sure it is done with affection, or at least not meanly. Occasionally I have done it here simply to save myself some time, if someone has a really l-o-n-g screen name.
It can also be, funnily enough, a sign of trust, as in, "I think we have developed enough trust that I believe you won't take umbrage". Thus my facetious (denoted by deliberately bad grammar or spelling) request to call zmjezhd zoom.
Face to face is different, I think. I would call someone by whatever they were introduced. If I met you as Latishya, I'd be very unlikely to call you Lat or Latty, etc. Though some people do, I have to say.
Maybe it's because in English we don't have a set way of indicating a close relationship, such as tu vs. vous in French. When I was in high school I met some Japanese exchange students; when I said "konchiwa" instead of "konichiwa" (sp?) to one guy, he blushed. Oops.