That's true. However emotional depth and character journey is mostly what makes a character complex and Johan lacks it, even if he shines in other areas (like a "Symbolic Character", as I like to call them).
That's not at all true and I explained why later. You can't really use development and emotional stuff on an antagonist. That doesn't really make sense. Johan, as an antagonist, doesn't need to develop. His depth is what makes him good.
It's indeed subtle, but the fact that it is not very much fleshed out in other ways than just being mentionned by other characters is enough to say that he lacks on that aspect compared to someone like Shiki whose concept basically revolves around her psyche.
It is fleshed out. The point is that it does it through more indirect methods by letting us come to that conclusion. The reason they don't go out of their way to make him seem like some tragic character is because he's the main villain of the story. He's supposed to be terrifying, not sad. He becomes sad once you finish it and think about his character. That isn't at all a good argument against him.
Shiki actually started by being emotionless and cold. Her character started to change when she met and fell in love with Mikiya with her actually caring about him to the point they had a child. Not to mention the other characters as well.
The point is that she has to capture our feelings. We have to care about her because she's the protagonist. Not that has to be super emotional or whatever
He fits his position as a symbol really well but so does Shiki, who also has her progression as a "human character" which makes her comfortably better imo.
That doesn't make much sense. Her having progression in her character as a protagonist shouldn't be a deciding factor over another character who also has that. Johan's journey is re-attaining his humanity and regaining his existence. That's his journey (hence why Monster ends the way it does).
While KnK goes quite in-depth into Shiki's psyche, I don't think it's a fair comparison to a story fundamentally based on delving into this man's psychology. It's two entirely different playing fields. Addressing psychology to make a layered and complex character and structuring a story specifically about a character's psychology give two different results. Hence why I think Johan is by far the better character.
But I'll just try understanding your argument:
-Johan lacks an emotional core (depth as you put it) while Shiki has plenty
-Shiki has better development as a "human character"
Those were the two main ones apart from some throwaway stuff like how Shiki was more layered (disagree with that) and how she was more complex (definitely disagree with that).
I'll just address them concisely:
-Johan's emotional core isn't supposed to be as blatant because he's the main antagonist of the story and is supposed to be intimidating. It's still there, but not as blatant as with someone like Shiki due to the different roles they play. It's a complete non-factor when comparing different characters.
-Johan's entire journey leads up to him regaining his humanity, and the story itself progresses towards the conclusion that Johan is human like other people. It doesn't develop him in the sense that you can feel a tangible change within Johan, but the perception of Johan from this inhuman monster to something far more human is done in a better manner, just due to the types of characters being dealt with.