The weapon was actively hidden during the cutscene. That part of the room was kept out of sight. The camera angles show a lot of weapons but deliberately show little of the entire room.
As for what Zenos will wield, it will not be a katana. He specifically says "there is one that I have been meaning to test", and Fandaniel responds with "well well, not quite what I was expecting". That dialogue would make no sense if he just picked up another katana. He's choosing something new to him.