* The size of the lexicon: The number of words considered "Greek" depends on the time period (Ancient, Medieval, Modern), the dialect, and the inclusion of archaic or rarely used words. Lexicons vary considerably in size.
* Word formation: Greek readily forms new words through compounding and derivation. New words are still being formed, even though Ancient Greek is no longer a living language in its classical forms.
* Variations in spelling and transliteration: Slight variations in spelling across different texts and transliterations into other alphabets can create discrepancies in counting.
To get a rough estimate, you'd need to consult a very comprehensive lexicon of Ancient Greek and then meticulously count the entries beginning with "Α" (alpha). Even then, the count would only be a snapshot of a constantly evolving language's vocabulary.