It was pure coincidence that Flarum displayed smiley emojis by default in previous version, there has never been any custom logic to define which emojis are offered by default. Those emojis just happened to be at the beginning of the list of all emojis. In the recent update we have updated the list with new emojis, and now the beginning of the list shows other emojis.
The list is part of an external library so we don't have control of the sorting of emojis. We should change the emoji dropdown to have a custom list of default emojis, but as I said above this feature has never really existed so someone will have to code it.
It might not be super intuitive but what the emoji button does is just insert the :
character which starts the emoji autocomplete. And I don't think this feature was really made to offer one-click insert, it's intended to search emoji. It would make sense to offer popular or recently used emojis as a quick select, but that's not a feature that exists in the extension at this time.