I think a lot of the food allergies (onions, dairy, horseradish) that are now under Common should only be common for, say, Medium lifestyle and higher. It seems pretty clear that for Low lifestyle you're eating soy-based crap with badly-synthesized flavours.
At Medium or above, though, I think you could justify having real milk or seasoning your food properly.
Common food allergies are all Middle or Lower Lifestyles IMO. Middle Lifestyle is the lifestyle of your normal wageslave, so it's not that far off. Plus, at Medium lifestyle, you still eat mostly Soy-based synthetics, just have a few "real" meals now and then. It's really hard to draw the line, to be honest, but I would probably draw it at the High Lifestyle. It's also difficult, because a GM needs to figure out what exactly most people are eating at their respective lifestyles, and what those foods might contain.
Onion could go under Uncommon, as it's probably not used often in the Shadowrun world. Dairy includes a lot of things, so I figure you would encounter it at some point, so that one is Common. Horseradish is (as far as I know) not expensive to grow, and I figure sauces and stuff are probably the poor man's substitute for real cooking. I figured the corps would just use it to keep the masses happy with their nearly unpalatable food.
Really, many things, allergies especially, fall under GM fiat. This is just a good starting point, your GM might say "Make it uncommon, I don't think it's common enough." And that's okay. They might also make you take a higher lifestyle to avoid your allergy (which means it directly affects you, so that karma isn't free). I think I'll stay away from Lifestyle dependence for how common an allergy is.
I will, however, move Onions and Dairy to uncommon. You are correct that they probably use non-dairy substitutes for many things that would be commonly made with dairy products. Keeping Horseradish common.
Thanks for your input!