The thing that jumps out at me is the cocoa butter.
Cocoa butter contains a high proportion of saturated fats, derived from stearic and palmitic acids.
Stearic acid occurs in many animal and vegetable fats and oils, but it is more abundant in animal fat (up to 30%) than vegetable fat (typically <5%). The important exceptions are cocoa butter and shea butter where the stearic acid content (as a triglyceride) is 28–45%.
What jumps out for me, and your cocoa butter idea is a good one, is the emotion involved in hot cocoa. It is an extremely pleasant, tasty, homey association with the past that could be such a good feeling that the feeling itself is what stimulates the brain.
Just a thought. It would be a mind over matter explanation and would account for the lack of success identifying a specific chemical compound.
Start raising kids where a beating or a severe lecture (Michelle Obama) is associated with drinking hot chocolate and the benefit might disappear in a couple decades.