That’s a very good question, mon ami, and no, you’re not crazy to question it.

You are correct in principle: I believe, on real ships, the wale runs continuously along the hull. It does not stop at the gunport. The gunport opening is cut through the planking and the wale. The wale is typically structural reinforcement; it wouldn’t politely stop and restart around a lid.
As for the hinges, the hinge straps were mounted to the outside planking (obvious), sometimes crossing the wale. If the wale projected, the iron strap would either bend over the wale, or sit slightly proud, or be mounted just above/below, depending on design. There was no elegant recessing; iron straps were mostly practical, but some were practical and decorative.
I think there is no need to rebuild: You can simply add a strip across the lid matching the wale (grain direction, important), thickness. Feather/sand gently, it will visually continue the wale line. But honestly, it is your call. I love her the way she is!
And the coper nailing is very convincing. The spacing is disciplined, the rows are consistent, and most importantly, they don’t scream “pattern” and match the scale. That’s usually the trap with simulated fasteners: too perfect, and they look stamped; too random, and they look chaotic. Yours sits in that nice, believable middle ground. You gotta love them!