I don't know jack about N64 emulators, but..
Any emulator that will make use of an PC analog stick ought to be able to make use of a 49-way. The resolution on a 49 way is considerably lower than on a true analog stick, though, so some games will play better than others.
This is the same in MAME- Star Wars and Road Runner are the easy examples. Road Runner plays fine with a 49-way, since the sitck controls how fast the bird runs based on how hard you push the stick. With a 49-way, the bird will only have 3 speeds (4 if you count "stopped" as a speed), but in real gameplay, how many different speeds do you need him to go? Star Wars, on the other hand, uses the stick (yoke, I know, but an analog stick plays exactly the same as the yoke, it's just shaped differently) to determine where on the screen you aim. Play Star Wars with a 49-way, and you'll find that there are exactly 49 places on the screen you can shoot, which means that some targets will be in space you cannot aim at.
You'll get the same thing with N64 games- try and use the Sniper Rifle in Goldeneye, and you'll find you can only aim at 49 places on the screen.