I suffer from this too particularly in the cold.
I have wondered if it’s the SPD/shoe combo as SPD’s don’t spread the load out on the foot as much as some other pedals do. Perhaps try some Look Keo pedals instead and see if that helps?
I also find that it happens a lot more on my Bianchi which is a very unforgiving alu frame (think old school Klein Attitude MTB type stiffness) versus my spesh Allez which is still alu but with the zertz inserts a much more comfortable ride.
EDIT: which may mean that it’s a combination of cold and the road vibration being absorbed by my foot (the right foot is always worse) leading to the numbness.