It's better to use 这个菜有什么原料? or 这个菜是用什么做的?
You see, 用料 is more written Chinese, and 了indicate that an action has been done, such as 我吃饱了. The emphasis of your question should be on 用什么, instead of the action 做.
If u visit a restaurant, u may also find these helpful:
1.有什么推荐吗?(any recommendations ?)
2. 点菜 (I want to order)
3. 买单 (check please)
4. 少辣椒 (less spicy, please)