It is a bit rude, but imagine you were in a normal game, clock nearby, your opponent hasn't made a move in awhile and you go, "Uh...hello? Anybody home up there?" The glare you would receive wouldn't be any different from our "Disable Chat" feature lol
So to more fully answer your question, it isn't exactly rare. More uncommon than anything. If they don't want to talk, let them be that way. Their choice.
Is it a common (or accepted) occurrence for one to stall and disable chat when someone speaks to them? I was playing someone in a 15/10 standard; he has stalled for at least 10 minutes so far and when I asked him a few minutes ago if he was there ("hello?"), immediately he disabled chat. It seems rather odd and rude.