It is "numerically" one because it is "counted" as one. The word "numerical" in this context comes from Latin translations of Aristotle, who writes in the Categories, Ch 5, 4a10–11 and 18–21:
"It seems most distinctive of substance that what is numericallyone and the same is able to receive contraries... For example,an individual man — one and the same — becomes pale at onetime and dark at another, and hot and cold, and bad and good."
Although there is some controversy as to interpreting what Aristotle meant, it was canonized in a particular way by medieval Aristotelians and spread into theological and legal discourse. For example, Aquinas writes in Summa Contra Gentiles, Book IV, Question 81:
"[T]he human body, over one’s lifetime, does not always have thesame parts materially... Materially, the parts come and go, and this does not prevent a human being from being numerically onefrom the beginning of his life until the end."
Morrison in Descartes on Numerical Identity and Time also discusses further developments, including Leibniz's identity of indiscernibles, and modern collapse of the distinction between numerical and qualitative identity.