Are the scores an overall average of all assignments and the exam or is it just the exam score?
Neither. It's the percentage contribution of your in-semester assessments + the percentage contribution of your exam mark. So if you have one essay worth 50% and one exam worth 50% and you get 70 on your essay and 75 on your exam, you get 0.5*70+0.5*75=72.5 as your mark for that unit. Scores round to the nearest integer I'm fairly sure, so you'd end up with a 73.
What is a HD average that people talk about? It is like when you score more than 80 in each unit or scoring more than 80% (overall 80% or more all units together).
On WES you should have a number called your WAM. Usually a HD average is when that number is 80+.
For some internal transfers, like the law faculty, a HD average is when the average of all your unit marks comes out to 80+. So if your first semester marks were 70, 70, 90, 90, then your average would be 80, and that would be a HD average. WAM is different to this though because first year units are worth less than other year units.