When writing helper tools for event handling, I have to write two versions, one for Node and one for Scene.

I suggest adding an interface with the following methods that both Node and Scene would implement (they already implement the methods anyway):

    <T extends Event> void addEventFilter(EventType<T> eventType, EventHandler<? super T> eventFilter);
    <T extends Event> void addEventHandler(EventType<T> eventType, EventHandler<? super T> eventHandler);
    <T extends Event> void removeEventFilter(EventType<T> eventType, EventHandler<? super T> eventFilter);
    <T extends Event> void removeEventHandler(EventType<T> eventType, EventHandler<? super T> eventHandler);

Also, maybe it makes sense for this new interface to extend EventTarget.