Shouldn't this really be translated as follows: "Had you never thought about that/it before?"
I have noticed that in other exercises in this series you have translated the Portuguese past perfect with the English present perfect.
Is this a mistake? Or are there times when the Portuguese past perfect is really the equivalent of the English present perfect?
(In my previous studies of Portuguese I had not noted this possibility in any of the grammars I consulted.)
I'm not sure if you are talking about Portuguese names of the tenses or if you are talking about the names Duolingo is giving for those tenses.
There is a "referential" difference between names given to the tenses in Portuguese and English. So, Portuguese "pretérito perfeito" is English "simple past" and "present perfect", and Portuguese "pretérito mais-que-perfeito" is English "past perfect".
In this particular case, Portuguese pretérito mais-que-perfeito is being translated not with English past perfect, but with present perfect. The tense is not matching, but I believe it's the most common way to ask this question in both languages.
In this example, it would have been much clearer if DL had used the past perfect tense in a sentence that shows its functionality, so that you can see that the "mais-que-perfeito" expresses the same time sequence as the "past perfect" - not the present perfect which is incorrect here.
• Você tinha pensado nisso antes... que você se foi embora?
• Had you thought about that before... you went away?"
Portuguese uses "pretérito perfeito" for the English "present perfect" and the "preterit"; both indicate a completed action in the past. The English "past perfect" is equivalent to the Portuguese "pretérito mais-que-perfeito". Daniel already explained this in his reply, but I thought it might help to provide a concise summary of what he wrote.
As I've noted before, there are times when English-speakers do not transpose the subject and verb for a question, usually in the context of a conversation in which the question is preceded by a statement. For example, Mark: "I didn't expect jumping off that cliff to be so dangerous." Marco (incredulously): "You had thought about it before?"