훈제 means cooked by smoking (훈 = the smoking process/method, 제 = making, manufacturing). 훈제 연어 (smoked salmon), and 훈제육 (smoked meat), etc. are fairly well known. 훈연 seems to mean the process of smoking or the smoke itself used in the process (I've never heard it used before). So it's a word only those involved in the process would know well.