Yes, you should mention this when making your ADRs. I asked a similar question here on the DIS and many suggested that I call Disney Dining back with my allergy specifics. I did, and the CM made notes on all of my ADRs (one at a time) and then gave me the direct telephone numbers with each of the restaurants. That way I can call before our ADR (24 hours before is recommended, but not required) and when we check-in, I can speak directly with the chef and will have my "allergy issues" (likely not as serious as your daughter's, but if I ingest almond or coconut I have to head straight to the hospital) addressed by the chef himself/herself.
I felt so bad having the CM go through all our ADRs (about 15 of them!) but she was wonderful about it!
Good luck!
Karen