Run the code:

    @Override
    public void start(Stage stage) {
        MenuBar mb = new MenuBar();

        Menu menu = new Menu("Some menu");
        mb.getMenus().add(menu);

        final MenuItem item = new MenuItem("MenuItem");
        item.setGraphic(new Rectangle(30, 30, Color.RED));

        menu.getItems().add(item);

        Button b = new Button("Remove graphic");
        b.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent event) {
                item.setGraphic(null);
            }
        });

        VBox vb = new VBox();
        vb.getChildren().addAll(mb, b);

        Scene scene = new Scene(vb, 300, 300);
        stage.setScene(scene);
        stage.show();
    }

Click the button.

Graphic node was not removed.