it is a stupid word from aristocratic times and deserves to die out.
It is even more widely used in Latin America countries, not referring to someone (especially if they are older) as Señor or Señora is very disrespectful.
I don't speak Spanish but as far as I know these terms mean mister and lady. Nothing wrong with that but sir has more to do with knights and a medieval worldview than with an egalitarian democratic worldview in which equal citizens meet each other eye to eye.
Like it or not, Starfleet is the armed forces of the Federation, they possess a military hierarchy, and military customs and courtesies.
I referred to the first post, Star Trek is inspired by yet not subject to stupid real-word military customs.
This is not a trivial matter because the beauty of Starfleet is that it is neither a club of scientists with flat hierarchies nor a contemporary military with all its obscene rituals and relations to violence. Something like Abu Ghraib is not the exception but the truth of the military. Back to Trek if we include Section 31 we have to claim of course that the obscene dark side hasn't vanished but merely been externalized.
Starfleet sans Section 31 is an organization with steep hierarchies that values discipline yet not brainless obedience and above all it takes its own rules seriously.