Why do we say "es la una" and "son las dos" (singular and plural) in Spanish, but say "it's one", "it's two" (only singular) in English?

I love questions like these because they get us to question why we say things the way we say them in both the language we're learning, but also more importantly, at least to me as a linguist, in our own language.

The answer to this question is quite simple in Spanish. Number-gender agreement: es la una (hora implied - feminine singular), son las dos (horas implied - feminine plural). Question solved!

More than likely, though, that didn't really solve the question. We're really wondering why Spanish respects number agreement with the verb to be, but English doesn't, at least in this case. The real issue, then, is to be found, not in Spanish, but in English! English usually does mirror elements linked by the verb be and other verbs in the same category, acting like an equal sign: 

• Jane = great boss > Jane/She is a great boss. 
• Pierre and João = happiest people > Pierre and João/They are the happiest people I've met.
• Rio de Janeiro = most beautiful city > Rio de Janeiro/It is the most beautiful city I've been to.
• Carlos = a new man > Carlos/He has become a new man.

To be is a linking verb, after all, but it seems to be doing something funny when telling time - we don't say "They are two in the afternoon", instead, we say "It is two in the afternoon". But, why?

That's because in English, time is a mass (or non-count) noun referring to the experience of duration, the totality of: Twelve hours is how long it took him to finish his homework. It's nine already! Five times is too much. (the totality of 5 times, not are). It's only two in the afternoon. 

However, time in English can also be a count noun, referring to multiple units: Remember the time (or the times) we slid because of the ice? Twelve hours were spent on that project. I told them to be quiet five times already, five! Two hours were wasted because we didn't follow the instructions! In other words, whether time is a count vs. non-count (mass) concept overrides number agreement of to be in English. Spanish is not the same language, so all of this extra baggage doesn't apply, and gender and number agreement has to happen as usual.

Finally, regarding "¿Qué hora es?" vs. "¿Qué horas son?", the second option is usually deemed wrong in Spain, because of tradition, not because of grammar. It's similar to the convention of "it is I" vs. the less kosher "it is me" in English. Both ways of asking for the time are perfectly fine grammatically speaking, but the plural option isn't common in Spain.

Note: If you are looking for a thorough review of how to tell time in Spanish, you may want to click here for a thorough review.