TBH, this is one of the many, many things about Mormonism that makes no fucking sense at all to modern sensibilities. Some Mormons do interpret it to mean zero caffeine, but that's not the official doctrine.

Honestly, the reason is very likely that, when Joe Smith Jr. was formulating his doctrine, there was a psuedo-science movement at the time that believed that hot beverages of any kind were bad for you. When you really start digging into the Mormon theology, it's clear that the doctrine JS Jr. was teaching was strongly based off of new religious movements that existed in the area, at the time.