There are other disadvantages to old, dark comb as well. It definitely discolors honey, but perhaps of most significance, old comb can be a reservoir of disease. Dr. Jaycox quotes Iowa state apiarist Glen Stanley's experiences. The Stanley outfit attributes better wintering and a great reduction in nosema incidence to routine comb culling. New evidence from studies by Nelson and Gochnauer in Canada also suggests that chalkbrood infection is less in new comb.
Old combs appear to stimulate fungal growth.
Although Dr. Jaycox doesn't mention it, a case might also be made for using foundation and newly drawn comb to discourage wax moth larvae. Dr. Jaycox encourages beekeepers to think about getting rid of old comb. Not all at once, but over time. He also suggests beekeepers find out for themselves the value of routinely replacing combs by doing some independent experimentation between colonies with black comb and those with newly drawn foundation.