I’m in the same boat as you, needing to take allergy meds every day for mold, dust, etc., but never really thought about its effect on the diet, mostly because I knew that even if it had a negative impact on my progress, I had no choice but to continue taking them.
I think they help more than hinder, personally. The keep the mucus production down, for one. I switched from the fairly mild Claritin (which I had been taking for years, but was slowly losing its efficacy) to Zyrtec after a month or so on the diet, and if anything I noticed increased improvement.
I’d like to hear if anyone has any research on this topic.