Hiya Monsterbuck from another Iowan! Yes the rub will reach the meat, the mustard is just to help with adhesion. It essentially "cooks away" in the smoker and you are left with the meat, the rub, and a really nice bark on the outside....
If you don't mind, why don't you shoot on into Roll Call and introduce yourself....cooking experience....type of smoker.....etc. This helps everyone here help you with any questions you have.....and we're nosey....heh.