Personally, I'd avoid the packaged mac & cheese until you have more definitive answers. I would not give it to him again, especially since he broke out in hives. His next reaction could be more severe and possibly life threatening. Both my kids have severe food allergies. Anaphylaxis (allergic reactions) can be fast, furious and life threatening. I don't mean to scare you but the possibility is there. Better safe than sorry. More info:
The Food Allergy & Anaphylaxis Network
I would recommend taking him to see an allergist. Our allergist doesn't do the skin prick testing until a child is at least 3, but I believe they may do a RAST test, which is done with blood work. Supposedly they are not quite as accurate, but can give you basic anwers. My kids have been through the prick testing several times and although it's not a picnic, it's not a big deal either. Quite helpful in getting answers and knowing exactly what foods to avoid.
As far as taking kids to the hospital... You do what you have to do as a parent. We've had a few ER visits with the kids due to anaphylaxis, severe asthma flares and/or injuries that required medical attention. None of them were fun for the kids but necessary. Heck, I just took them to the ped. today and my DD (10) needed her finger pricked to test for anemia and a chicken pox booster vaccine. You'd think it was the end of the word with all the drama she exhibited.
I was empathetic, but made it clear she had to do it.