Yes, medals are usually in larger competitions awarded completely independent of the scores. Here's what happened at the NHC Second Round (and at other big comps including the first round) - it's usually referred to as a miniBOS.
The category is split between judging panels. For instance, I judged 16 Belgian and French Ales in Seattle. There were 3 judging teams of 3 judges a piece. Each team tackled individual entries. (It ended up being about 13 entries per team). Each team determined what the top 3 beers were from their portion of the category.
Those 9 entries were then re-poured (from a fresh bottle) for the 3 head judges of the flight teams. (aka 1 person from each squad). We know the entry number and the style, but not the score given by the previous judges.
We debated the merits of each entry and eventually winnowed it down to our top 3 beers for the flight and their medal order.
So why the score independence? Because as best as we try, different judges grade differently. A 38 from me would be the equivalent of a 42 from another judge. If you just go by score, then entries judged by my crew suffer.
Now in smaller competitions and/or smaller categories if a single team of judges can tackle all the entries together then yes, medals are usually based on score. (Although judges usually have the right to assign whatever order they see fit)
