An advantage of leaving them as "unknown", is that you will get sentences each time the word appears in a quizz, so better internalizing it in context. If you know it perfectly, just that you don't use (I know 切腹 and 真言 for example, yet I have never used them in a sentence) and only want to remove the "red underline" in renshuu sentences, then defining it as know is a good idea.
