Cycling shoes have a low profile, so they are inherently not orthotic friendly. In order for a cycling shoe to comfortably fit an orthotic it essentially has to have a removable insole. A removable insole allows the placement of the orthotic with no problems. There are not many cycling shoes that feature a removable insole, so below I have listed cycling shoes that I found are orthotic friendly in that they have a removable insole.
Keen Arroyo Pedal Cycling Shoe– These feature a removable EVA insole, and this shoe also has the depth for a shoe that would be orthotic friendly.
Cycleur de Luxe Crash– These shoes have removable leather insoles, but do not have the depth of the Keen Arroyo. However, if you are a competitive or intense cyclist this is a superior cycling shoe.
Shimano SH R088– These shoes feature a removable footbed which is the same thing as a removable insole.
Brooks Ravenna 5– This shoe is similar to the Keen in that it has the depth as well as the removable insole to fit an orthotic.