However, option B will make the better joint. With option A, the neck is only making contact with wood at two points, the rest is varying levels of glue, and the glue is strongest when there's not much of it and it's bridging a small gap.
It's never a good idea to have thick pockets of glue if you can avoid it. The strongest joints are made using the thinnest layers of glue. Why do you clamp pieces of wood together when you glue them? To both force the glue into the wood and to get the glue layer as thin as possible. Otherwise there wouldn't be any point in clamping joints and you'd just lay one piece on top of the other and wait for the glue to dry.
A good glue joint is stronger than the wood itself. Although your shim is thin, when glued between two other bits of wood, the result is still a strong joint.
It's something you can try yourself by glueing a piece of veneer the length of the pocket between two 25x50mm lengths of timber in an overlapping joint, clamp tight and let it dry for 24 hours. Then clamp one bit of wood and try pulling on the other bit of wood.