It never specifies in the Doctrine and Covenants Section 89, Why we are discouraged from drinking "hot drinks" which Joseph Smith later clarified as "tea and coffee." 
 
It's not because of the caffeine.  
 
I really think it's because God told us not to. Just like the Jews can't eat certain meats unless they are prepared a certain way. Is it because they are bad for them? No. It's cuz they believe that God told them not to. It's along those same lines.  
 
The Church of Jesus Christ of Latter-Day saints has never issued a statement "officially," discouraging the drinking of drinks that contain caffeine. They do offically discourage drinking tea and coffee.