The pressure at the open end is equal to that of the atmospheric pressure. So how can it be a pressure node when the pressure is not 0? It is the atmospheric pressure.
Edit: Is there an intuitive reason for why the open end must be equal to atmospheric pressure?
When we are discussing the pressure in a pipe we are referring to the gauge pressure. This is the pressure in the pipe minus atmospheric pressure.
So when we refer to a pressure node we mean the gauge pressure is zero i.e. that the pressure at a node is equal to atmospheric pressure. And since, as you correctly say, the pressure at the end of the pipe is 1 atm that means the gauge pressure at the end of the pipe is zero and therefore that there is a node at the end of the pipe.
