Because it's irrelevant, and only advanced as an argument on this issue by people who fundamentally misunderstand what religion is and how Section 2(a) of the Charter works.

Section 2(a) is a personal right, meaning that it is grounded in the religious beliefs of the individual.  If a Muslim woman sincerely believes that wearing a niqab is a religious requirement (seeing as there are many different interpretations of Islam, just as with all religions), that's the end of the inquiry.  Just as, if a Catholic sincerely believes that something is a religious requirement, the courts don't send a request for clarification to the Pope.

Moreover, all religions have aspects beyond those set down in their holy texts.  There's loads of Christian doctrine not found anywhere explicitly in the Bible.