他日语讲得很流利。 can mean both "He speaks Japanese fluently." or "He speaks Japanese very fluently."
We habitually add 很 in sentences like this just to make it sound natural/better(I don't know why.) Therefore, it doesn't necessarily mean "very" here.
If you only say 他日语讲得流利。without 很, it normally implies that you are likely to add more content after that sentence, like 他日语讲得流利, 汉语更流利。or 他日语讲得流利,他哥哥讲得更流利。,etc.
If you want to say "He speaks Japanese "very" fluently." in one sentence, with the emphasis on "very", you can try to use another adjective, like 非常( it also means very), 十分(also very), 相当(fairly),超(super), etc。 People will feel the emphasis on "very".