Does smoking while taking doryx (doxycycline) cause it to not work and side effects to occur?

No effect on effect. Smoking would not be expected to change the effectiveness of doryx (doxycycline). If smoking and Doryx (doxycycline) both upset your stomach, one could make the other more distressing, but i doubt you'd be smoking if it routinely upset your stomach. You shouldn't smoke anyway! stop it now and save a lot of healthcare dollars and misery later.