(Why wouldn't you go home at the start of the break? We stopped work for an hour. Then, when that hour was over, even though we were still at work, we went home. If you are going to leave immediately after the break, just leave when you start the break.)
I will be home in an Hour. "An" already indicates the quantity of one.
I guess that in the other cases of "a one-hour break" the "one-hour" is working like an adjective that modifies "break" and the article "a" is for the "break" in itself, making it (one) break. Hope that makes sense.