Hopefully someone with some specific BCN experience comes along. But the generic answer from my experience is that it’s normally fine if the desk stays open all day, but it’s never guaranteed so be polite and smile when asking! Also you may be asked to give priority to passengers on an early flight if they are pulled forward from the queue.

The one major exception I can think of is Geneva on weekends in ski season due to the ability to store such large volumes of baggage and the fact that lots of tour operators drop people off very early.