Official comment
@Dominic > The hot cue behaviour is mimicking that of the CDJ; when you press it, the player continues to play. Many users have asked for the alternate method, where the function follows the action of the player -- if the deck is playing, the cue will play, but if the deck is paused, the cue will remain paused unless the button is held. We hope to see this included in a future update of the software.