It's an easy decision to make the plural fistulae rare. It's used much less often than fistulas, and mainly in academic publications. But what of the singular word fistula?
As the comments indicate, the word is known to quite a few people for various reasons. However many others evidently are unfamiliar with the term.
One type of fistula, the obstetric fistula, is an injury that can occur during childbirth, usually resulting in a stillborn child and a severe lifelong affliction for the mother. This problem has been largely eliminated in Western countries, but is all too prevalent in some poorer countries. The website yelnats linked to is run by an Australian based charity working to eliminate the problem in Ethiopia.
So it would seem likely that the word would be more frequently used in some countries than others. This is borne out clearly by the News on the Web corpus. This corpus collects massive quantities of text from English-language news media in many different countries. This shows that the most frequent occurrences of fistula and its plurals, per million words of text, are in Tanzania, Nigeria, Kenya, Bangladesh, Ghana and Pakistan, in that order. Usage in the US, UK, Ireland, Canada, Australia and New Zealand is much less frequent.
It seems to me that fistula should also be treated as a rare word from now on.