Well, right off the top of my head and without checking out anything offical on this…
I think they were hiding out too because, afterall, the Holy Spirit hadn’t decended upon them yet and they were scared for their lives, look at what was happening to Jesus. I would imagine they were thinking that if this could happen to them, why not them too?
Remember when Peter was denying knowing HIM?? He was scared, right?
I think that John just stuck by the Blessed Mother, he was the beloved one, he wasn’t as afraid as he was compassionate and sounds to me like he had more courage since he was young (you know how them youngsters think they are invincible and that nothing can happen to them.) He was probably given a special grace by God since he loved Jesus and the Blessed Virgin so much. I always thought that he probably stuck by her to console her and just stand with her and be there for her. He probably thought of her as a Mother…(and wasn’t he wonderfully rewarded for that from the Cross…as Jesus proclaimed…Behold Your Mother…Behold Your Son.
The upper room could have been where the Apostles were. Was that where they gathered with the Blessed Mother in prayer before the Holy Spirit decended upon them after Jesus went back to heaven? (I’ll go read Acts and see what it says about that.) Or maybe the OP is right, maybe they hung out in the crowd, hiding out and watching from a distance. Do we officially know? Good question.