They usually have a sense of the unknown and the hidden. Witches often have secrets, and the mystery novels are about uncovering those secrets. In 'The Witching Hour', there are generations of family secrets that are slowly revealed throughout the story. And there's often a spooky or atmospheric setting, like old houses or dark forests, which adds to the mystery. Take 'Practical Magic', the Owens' house has its own charm and mystery.
Most witch mystery novels also have complex characters. The witches themselves can be both good and bad, or morally ambiguous. In 'Hex Hall', the characters at the school have different motives and powers. And there's often a battle between different forces, like good witches against bad witches or witches against non - magical antagonists. The mystery then unfolds as the characters interact and the power dynamics shift.