We had those questions on our application as well -- did we want to specify hair and eye color? We put "any" on both of those boxes. DH has blue eyes and dark blonde hair; I have dark brown eyes and brown hair, with sorta olive colored skin. So we felt we had the bases covered!
In the end, we wound up with 2 blonde-haired, blue-eyed children that look exactly like one another (even tho adopted over 500 miles and 18 months apart), and look nothing like me. I get questions when I am out about whether my husband has blonde hair (primarily b/c my kids are SO blonde). I am glad that my kids look like one another so that they can choose to share or not tell their adoption stories -- they are not obviously adopted (they will be 2 years apart in school, so they will share the same school often).
I would not have felt comfy specifiying characteristics... you hit it on the head: we'd be special ordering kids, and that makes me a bit squemish.. Just my opinion, tho. If DH and I and DS all had blonde hair and blue eyes, we may have specified our daughter share those characteristics to minimize the differences she may feel. But that was never something we had to cross.
Hope that helps!