The point, my dears, is not whether or not there is any definite scientific evidence which points in any particular direction. Science is not always conclusive, and (especially in the case of coffee) has ofttimes disagreed with itself on the health aspects of these substances. 
 
Yes, the fact that these substances are addictive plays into the decision to abstain from them. Many LDS people take this a level further and abstain from or curb use of as many addictive substances as they find -- cf. Mormons who don't drink Coke, Pepsi, or other caffienated drinks.  
 
However, the real issue at hand is the fact that we have received a commandment from a source we consider to be extremely trustworthy, and we will follow it; indeed, is it not written, "faith is not to have a perfect knowledge of things"?  
 
Of course, this brings up the topic of blind faith -- which none of us (intelligent) LDS agree with. We are proponents of personal revelation, whereby anyone -- member or not -- may pray about something and seek to know its veracity (or to use LDS terminology seek to "gain a testimony of it"). 
 
Hence, upon learning of the Word of Wisdom, conscientious investigators seek testimony of it. The WoW is just as much a test of faith as it is for our health. 
 
If you're still having trouble, consider the Mosaic Law, which prohibited the ancient Jews from consuming pork or other items which were not kosher. Was it for their health? It almost certainly aided them in this regard, as pigs are extremely dirty animals and will consume, quite literally, almost anything. However, it was the test of faith which it represented that was most important. 
 
*bows, exits stage left*