Thanks for your question about cobblestone throat. I presume you know what that means but just for everyone out there, the cobblestone throat is used as a appearance of the back of your throat due to the enlarged areas of lymph gland tissue (follicles).
You didn't mention what symptoms you are suffering from because you are thinking that they may be giving you an afternoon throat. These lymph gland follicles react to different factors in the environment and enlarge in response to them.
The simple answer for you to stop smoking. Repeated courses of antibiotics won't really do you much good. It is worth coming in for a proper check-up by an ENT doctor, as this chronic irritant may be making other areas of your throat flares, which might be an incidental finding noted by yourself. Smoking, as you are aware, contains carcinogens (cancer-causing substances)!
Stop smoking, regularly exercise, have a balanced diet which includes lots of fresh fruits and vegetables, and I'm pretty sure your cobblestone throat problem will improve.