Translation:Is the train not here yet?
And you might hear a native English speaker say "is the train still...?", but that's non-standard English--asking a question by leaving the last words out for the listener to fill in.
I answered "Is the train here yet?", seemingly the opposite question, but Duo still took it. Go figure.
As commenters above have pointed out, まだ is so commonly used with negated verbs/adj., that this phrase just leaves out the verb: "has the train [not arrived] yet?". I suppose that it could, contextually, also mean "has the train not left yet?".
However, if you want to say "still is", you should probably add a (positive) verb: 電車はまだあるか
I don't think that's a correct translation, but I put "Is it the train yet", which should really be correct even if it's a slightly unusual way of putting it (you might ask that if there was some noise or indication that something was nearby but you weren't sure what). The word 'here' isn't in the Japanese.
Under most circumstances, yes. In this case no, not in the Japanese sentence. "Here" is ここ btw (short o's: koko), and as previous comments have pointed out, the literal translation of the Japanese is indeed "Is the train still/not yet?". There's no "here" in the Japanese sentence either, because it's implied.
In Japanese, this is an acceptable way to ask about the train's arrival status. Saying something like "is the train yet" in English would be completely ungrammatical though. So the two sentences are not literal, word for word translations. Same goes for many other Japanese sentences (plus, every language has things like this to some degree).