I'm making a small top-down adventure game and have been wondering about how to handle rooms. For the game, I would like to travel from room to room by room transitions, creating a similar effect to some of the older Zelda games. initially, I built out the world in one scene due to it being relatively small but the more I look at the less I think room transitions would work. Should I create a new scene for each room or stick with what already have and use something like Area2ds to divide rooms

Well, it probably would benefit you to have them as scenes, but I'm not saying you should use change_scene_to_file or anything like that. It just helps for having them organized and reusable. You can still have them already instantiated as nodes in your main scene.

As for transitioning between rooms, exactly what kind of transition were you thinking of? The kind where the camera tweens to the next room? That would be perfectly doable whether you have your rooms as scenes or not.