One common theme could be the exploration of their different personalities. Jack Frost is often seen as more carefree and mischievous, while Bunnymund is more grounded. Their relationship in the fanfiction might play on how they balance each other out.
Well, in 'jack frost x bunnymund yaoi fanfiction', the theme of discovery is quite common. They discover new aspects of themselves through their relationship with each other. Also, the theme of acceptance, not just of each other but also of their own feelings which might be new or unexpected. And sometimes there's a theme of adventure where they go on quests or face challenges together, which in turn strengthens their bond.
A frequent theme is probably the overcoming of differences. Since they come from different 'mythological' or character backgrounds, the fanfiction may focus on how they deal with cultural or elemental differences. For example, Jack Frost with his ice powers and Bunnymund with his connection to spring and earth. Another common theme could be the development of a deep emotional bond that transcends their initial misunderstandings or rivalries.