When counting, the Greeks (like everyone else) obviously used their word for “one”; they did not read the names of the letters that were used as numerals (α´, β´, γ´ etc.). It could be debated which gender they used when counting. Presumably, when counting specific items they would have used the gender of the thing in question. For simply counting in an abstract way maybe they used the masculine (like Russian один), maybe they used the neuter (German “eins” is etymologically neuter, though in modern German used only as a number name); two-gender languages seem always to use the masculine (French “un”, Arabic wāḥid etc.).The modern Greeks use the masculine έναςneuter ένα, if that is anything to go by.