He is often called Blue 1 while working together with Blue Team, just like Noble 6. Some also call him by Sierra 117 in the games.
Also sometimes just 117.
It's also just very common to call people by their rank, they call generals general, captains captain, sergeants sergeant doctors doc etc. But most people didn't really know Johns real name, at least not in the earlier spartan era. But even if they did, they might not use it. There is a culture in some lines of work and in some countries more than others, where it is disrespectful to call some people by their first name, I come from a country where we call pretty much everyone by their first name, teachers etc, so it's a bit alien to me, but for example in US military that's probably what it's like "ish" (Don't know to what extent though, correct me if I'm wrong). I think the UNSC is very based on that culture, and very based on the US military. They call Captain Keyes either Captain, or Keyes, or just Sir but rarely Jacob, unless they are his personal friend, same with Sergeant Avery Johnson etc. But Chiefs sirname is "classified".