To achieve a band 6 for any subject, do you have to get 90/100 in the HSC exam?
If we're talking about raw marks, no.
Alignment is a process that the BOSTES uses (you can research it if you want) to address the fact that different courses have harder exams in different years. A board of members called 'judges' are responsible for determining the alignment algorithm that gets applied that year.
Because the algorithm is different, it is never possible to say with certainty how much you need to score raw to get aligned to 90 (or whatever mark in question). As per the raw marks database, however, historically it is approximately 83. Subject to about plus/minus 4 inaccuracy.
Post-alignment, however, you must have achieved at least an average of 90. This average is between your moderated AND aligned internal mark, as well as your aligned HSC exam mark.
For further reading, find Jamon's article