Thumping is tied to more than just a rabbit being scared. It pretty much has to do with them feeling strong emotion. So when they are scared, on alert, irritated, and yes, even happy.
Usually when they are thumping because they are scared, they will also freeze in place or run and hide, and their ears will be up and alert(for uppy eared rabbits) and their eyes will be wide open. When they are happy and thump, they will just run around continuing to play. Some of my rabbits will thump too, when they are running around playing.