The Chart components does no have a pseudo-class "disabled". For almost every JavaFX component the style is "-fx-opacity: 0.4;". I think ".chart:disabled," should be added to the modena.css.

Example:
import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.chart.LineChart;
import javafx.scene.chart.NumberAxis;
import javafx.scene.control.TextField;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class RunTest extends Application {

@Override
public void start(Stage primaryStage) throws Exception {

TextField textField = new TextField();
LineChart<Number, Number> chart = new LineChart<>(new NumberAxis(), new NumberAxis());
VBox vBox = new VBox(10, textField, chart);
vBox.setDisable(true);

primaryStage.setScene(new Scene(vBox));
primaryStage.show();
}

public static void main(String[] args) {
Application.launch(args);
}

}