I don't know for sure, but if I had to guess, I'd say a 49 way would be capable of directing your character not only to 0o 45o 90o 135o etc., but also 7o 15o 22o 30o 37o, and so on...
I'm pretty sure that 49 ways are infinitly more difficult to encorperate with a computer and are only used for a handfull of games too.