The great lakes are massive bodys of water so its almost impossible for people to eliminate all of them, the only way they could disapear is if they hybridized with walleye.
People find species that were thought to be extint all the time. Animals that live in a massive area that get hunted out or in this case get fished out will move to other parts of the area.
Yes food and climate can change the apperence of the fish but not drasticly.
I bet if you caught 10 walleye out of lake Erie and DNA tested all of them, some would have blue walleye DNA present.
Ive also heard they stocked blue walleye long ago in different bodys of water in Canada, Wisconsin, Minnisota.
The blue walleye is just an adaption of a normal walleye where one dominant trait in certain fish survived and breed with others untill they populated the lakes. Probly started of as just a color morph that blended in more and was less likly to get seen by predators then a normal walleye.
Just like the great Lakes muskie compared to other strains of muskie it just hasnt adaped for a long enough time period to be a subspecies.