It has nothing to do with not fully appreciating the problems it causes computing systems - many of these notations predates the existence of computing systems or even the though of them. Mathematicians use both zero based and one based systems, sometimes due to mere convention but more often where it is natural to the problem domain. Natural notation has a lot of power to help understand your results. I agree sometimes it is a pain to translate to a physical representation in a computer, but it's not like "just always use zero based" is a good enough answer either.
