We are not talking about security checkpoints but about verifications at the gate.You have to remove everything from your pockets and it all has to go through an xray machine. What does this mean? It means that they WILL see your phone. The xray machines can see the internals of your phone in many cases, so it would be easy enough for them to have a schematic of the internals of a Note 7 there for reference and taken closer look if they think one is a Note 7.
Some airlines have also indicated that they will make an emergency landing if someone does have a Note 7 on board somehow and that the person who brought it on board would be responsible for all associated costs, including other passengers delays.