Why "Where are boats" is not accepted? I know it has an article in German and that is for practice, but it doesn't make much sense in english to put "the" there and besides, on some examples it's not required to put an article in English even though it's there in German/French/etc.
You can't let out the article here, because just like in the German sentence, this refers to specific boats. Like someone asks you if you want to take a boat ride with your friends and you are like "Yeah sure, where are the boats (which we are going to take)?". If you ask where ANY boats are, you drop the article in German and English.
Yes, your sentence is a better way to say it. I still think the sentences you mention are also correct in English, although I agree it is very unusual in both languages. After rereading my old comment, I have to say that this was not supposed to be a definitive statement on how you have to form sentences like these. My answer was to explain that you have to consider that we talk about specific boats, so I would like to add that a straight dropping of the article might not create usable sentences in every case.