I'm guessing that the 2% is chemicals that actually do what the product is supposed to do, like clean, tone, be a shampoo etc. I'm guessing Aveda is probably one of the pioneers in the natural products arena, before all the other companies have popped up with their own natural (and often organic) products, and though it's not completely natural, it's good enough for most people and at least it works. Honestly, how many of us can say our all-edible, all-natural stuff we make at home works super duper, smells good, and actually has a shelf life more than a week without getting bacteria in it?
And yes, people can be allergic to anything, especially natural essential oils and botanical chemicals. Some of the reason why commercial products went non-natural to START with is to get rid of some of the allergies and to keep costs down.