There are numerous reasons for using a gamepad over a keyboard, which defeats the "then there's no point in using joy2key" statement. First off, keyboards suffer numerous I/O errors not present in a gamepad. Pressing Z, X, the up arrow key, and the right arrow key at the same time will cause an I/O error, for example. I think ZXCV or ASZX (my typical NeoGeo and SNES layouts) will cause an I/O error if pressed all at the same time. Whereas with a gamepad, you can press all the circle buttons at the same time without any errors. Also, joy2key is meant to override not just the keyboard but the mouse as well, so people who are used to console gaming can play mouse-and-keyboard games (or even straight keyboard games like Doom or Quake 1) with an input device they're more comfortable with.
That and you can program macros (in the Jap version of Joy2Key, and also in Logitech's own driver).