I think another acceptable rearrangement of the sentence could be "我们今天晚上会吃日本菜吗？"

What about "我们晚上会吃日本菜吗“ ？ （leaving off 今天）

In Chinese, either the time or the subject can be at the beginning of the sentence. The answer above and 我们今天晚上会吃日本菜吗？would both be correct.