I understand this question in two ways. One, why do we not consider this factor in applying the laws of Nidda, and second, why did the Torah not provide an exception to the laws of Nidda for infertile women?
As to the first question, as a general rule the reason behind the law does not affect the application of the law.
There are two reason for this. One, we can never say what the true reason is, or know if there are not other reasons for the law, and maybe the reason given is actually incorrect. (See Mishna Megilla 4:9, that we may not ascribe God's kindness as the reason for Mitzvos.) Second, even if we could say definitely that a given reason is the true reason for the Mitzva, the Mitzva is not the application of its reason. The reason is a motivation for the Mitzva, but the Mitzva is always defined by its rules.(Also in law, the language of the law is what is binding, not the motivation behind the legislation.)
As to the question why would the Torah not have an exception for women who cannot conceive, there are a few possibilities. First, the reason of Niddah being about the loss of life-giving potential may be incomplete, and there may be other reasons for the Mitzva. Maybe it should be understood in a different way. Possibly the Torah saw fit to make a general rule that applies to all one, even if the reason behind the Mitzva does not apply to their specific case. ("לא פלוג" in Talmudic reasoning).
More practically, before modern medicine there was no way to know if a women could not conceive because she was not ovulating, or for any other reason, so it would not be possible to have a rule based on this.