Some people are also allergic to onions. My DH works with someone who just smells them and her throat starts to close. She's been to the hospital a few times this year b/c someone put onions in her food by mistake.
Since so many people have food intolerances/allergies and because Disney has a good reputation for handling them, they may be looking for menu items that are going to be edible by more people.
I don't think that's why they don't have them in some places because if that were the case they wouldn't have them anywhere on property. Also, if they were that concerned about allergies, they probably wouldn't use nuts.