Shades conceal one of the things which makes up your disguise. If people can recognize your undisguised face while you have shades on, then I'm not sure why hiding your fake eye color would not make it easier for you to be recognized.
I know the game code doesn't know the difference, but the game code doesn't let you use shades (without contacts) to enhance any disguise either.
Hoo boy... yeah but anyway I wasn't asking why should we fix this, I was asking why you'd ever hide the contacts. Just because you would if you could, I guess?
Oh no wait... there's actually a really good reason to wear shades over a disguising item.
Style > substance.