You say that to someone when he arrives too late, usually when you are a bit upset with that fact. For instance, if you agreed with your friend at 8 and he arrives at 9 you say it (also you ask for an explanaition :P ) Hope I help you a little :)

As others have said, it's an expression used when the other person has arrived very late. It's similar to English "it's about time!". If the construction confuses you, I'd like to point out that "vaya" here isn't really a form of the verb "ir" 'to go', but rather it's closer to being an interjection meaning "whoa". If it helps, I would literally translate the expression as "whoa, what an hour for you to come!" (but note there's no pause in Spanish after "vaya", and "horas" is really in the plural).

It's an expression referring to someone that has been late to somewhere

It mean: Why are you arriving so late?

Esta es una manera de reclamar a alguien su falta de puntualidad.