Since the negative inflection is on the auxiliary verb "had", the if clause is most likely to be interpreted as a case of 'primary verbal negation', and hence it is a negative clause:
If you hadn’t [studied hard] and [got good qualifications], you might have ended up in a boring, low-paying job
I've bracketed the two coordinates which form the main part of the VP, from which I think we can assume that the meaning is If you hadn't studied hard and if you hadn't got good qualifications. The second coordinate has to be governed by the negator otherwise removing the first coordinate and its negator would give the unintended meaning If you got good qualifications, you might have ended up in a boring job.