Unfortunately, I don’t speak Ancient Greek. So I can’t be sure, but your phrase sounds like some kind of misconception.
Yes, every natural language has many ‘illogical’ things that appear to be perfectly logical when you learn the history of the language. But Ancient Greek was a natural language too. As a natural language, it also had many ‘illogical’ things that appeared to be logical when you learned its history — Ancient-ancient Greek or Proto-Indo-European, and so on.
As for using the same symbols for writing words, numbers, and musical notes, this seems to have no relation to the language itself.