No, as Masaken mentioned above, it is not a disadvantage to take subjects that are considered more difficult. This is because the HSC system is largely based on a student's performance relative to that of other students in their cohort in a particular subject as well as the state's performance in that subject, where all students will be exposed to the same level of difficulty imposed by the subject, and will have to rank as high as possible relative to their cohort to ensure favourable internal performance, as well as having to perform at the best possible level in the HSC exam. This is so that their overall HSC mark is sufficiently high so as to place at a sufficiently high percentile that will ultimately enable them to achieve their desired ATAR
However, taking a subject that you are not fully confident that you can perform well in could place you at a disadvantage in the sense that you may not be able to perform at a sufficiently high standard that would lead you to a favourable result in the subject. For example, if a Mathematics Extension 1 student wishes to take Mathematics Extension 2, despite unfavourable performance and their teacher advising against it, they could be placing themselves at an inherent disadvantage performance-wise.
I hope this helps!