They won't know you have allergies unless you tell them at the physical. No kidding, there is no test they will give you to determine whether you have allergies or not. So as long as you aren't sneezing or sniveling at your exam, all is good.
Now, here is the real problem..You aren't allowed to self-medicate in the AF. So, if you have symtoms, you have to go to the doc and say you have a "cold" or something. You will be grounded until you get "better". If you get busted taking OTC meds, it's hasta la vista, baby!
I had allergies in my home town, but when I moved to different locations during my carreer, my symptoms dissappeared. I guess it's related to what you are allergic to and what location you live in.
I know this all sounds like heresy, but I wouldn't have had the great carreer that I had if I would have played it 100% straight. I made it to the rank of major and flew KC-135s and T-37s.
Like I said earlier, the AF will prescribe allegra if you have allergies, and come to think of it, prescribed it to some of my students in pilot training (I was a UPT instructor at the end of my carreer). The students claimed that they never had allergies before, but moving to the pilot training base, they developed symptoms. This sounds like a reasonable story since some allergies are environmental. These guys had to sit for two weeks to see if the allegra had additional side effects, but then were put back in the training flow...end of story.
Good luck. I hope you understand what I am telling you and will gladly communicate further if you would like.