The cones contain no pollen. But they are full of resin as are the bark and the needles. He might have reacted to that. You could test that with a tiny drop of resin.
I think in this case it would be worth making a thorough test and if possible try an immunisation as pine wood is often used for building furniture.
My son started to outgrow most of his allergies in his teens and now (at the age of 32) only has the occasional mild reaction to things that used to cause a severe reaction.