In the Matrix, why is the Oracle’s message “Know Thyself” in Latin, instead of the original Greek?

Because Latin was always better known in the West than Greek. Greek proverbial expressions are almost uniformly quoted in the West in Latin; e.g. Deus ex machina, not apo mēchanēs theos; Et tu Brute, not kai sy teknon; quod erat demonstrandum, not hoper edei deixai.

Gnothi seauton seems to be as prevalent as nosce te ipsum for Know thyself, if you add up transliterations and Greek script on the Googles.