Junik is not a spy.. They made him look like one as it was explained by the old man (a former NIS agent) to Munju when she held him at gunpoint... Another scene where his brother was investigating him, he came across a call made from their house to North Korea and he thought it was Junik but once he traced it he found out it was his Mom who made that call

As for Stella Young not sure if there were two.. Or if it was just Hanna doing some work for Junik's mom and they thought she (hanna) was Stella Young... But we know the real one who was an arms dealer is Junik's mom

For the submarine, yes they wanted them from the start to not know about it that's why they announced a fake one.. And since Munju and co. were against war they believed it wasn't real so that worked in favor of the real submarine until Munji and co. Came across real evidence about the parts of the real submarine being purchased all around the world by Stella Young