Medicals didnt include an eye exam for me so I dont see how that could even make it into your file, assuming all exams are roughly the same.
Also, from what I understand, the goal is to find out if somebody has a chronic or serious condition that could either be a health risk for the public in canada or could put a large financial burden on the country.
Neither one of those would apply to colorblindness so you shouldnt worry about it.