It has to do with the amount of power usage and the return rate or mine rate of LTC/BTC. AMD seems to have a better ratio of coin per wattage. So basically just better bang for the buck.
The reason, more or less, is that AMD GPUs tend to have way more cores than Nvidia GPUs, and their cores can, in hardware, do the integer operation necessary for the hashing algorithm. Nvidia can only emulate the integer operation, so it takes three instructions on Nvidia vs one on AMD.