Let's not take the present out of the present perfect!
The question "How long...?" assumes that the applicant is still studying English, no matter whether the application asks the question using the present perfect (Sentence 1) or the present perfect progressive (Sentence 2).
The present perfect often refers to a action or condition that started in the past and continues to the present. As such, it does not leave open the possibility that the situation is no longer true at the present time. This is especially true with the interrogative "How long...?"
(1) How long have you been here?
I have been here five minutes.
(2) How long have you and Sam been friends?
--I have been friends with Sam for six years.
(3) How long have you lived in New York?
--I have lived in New York too long.
This construction does not leave open the possibility that the situation is no longer the case in the present. The same is true for
(4) How long have you studied English?
--I have studied English for six years.
Consider some alternative but illogical (and thus ungrammatical) possibilities:
(5a) How long have you studied English?
*--I have studied English for six years, but I am not studying it now/anymore.
This is as illogical and ungrammatical as
(5b) How long have you been here?
--I have been here five minutes, but I am not here now.
(5c) How long have you lived in New York?
*--I have lived in New York nine years, but I no longer live in New York.
(5d) How long have you eaten peanut butter?
*--I have eaten peanut butter for six years, but I have stopped eating it.
For (5abcd), the person answering the question can use the simple past or the past perfect if the situation is no longer true.
There are other contexts in which the present perfect can only refer to situations that began in the past and are still true at the time of the statement (I have lived in Chicago since 2010).
In addition, the present perfect progressive can refer to actions that are no longer true at the time of the utterance (e.g., Where have you been? --I have been running) or (it has just been raining).
Therefore, I prefer Question 1. To me, the past perfect has more a sense of immediacy than does the past perfect progressive. I suppose its lack of the verb "been" + the -ing form has something to do with this. Plus it is shorter and easier to say.