It doesn't matter which orientation you mount the joystick UNLESS you have one like a 49-way or a perfect 360 (and maybe others). In those cases, it can still be mounted in any orientation, but you'll have to adjust which wire goes where because it's 'set' as to what direction is 'up' 'down' 'right' and 'left'
In any case, it's not a big deal. I mounted the perfect 360s in my cocktail cab 'sideways'. I just had to figure out which terminals to attach which wires to since the R, L, U, D markings were no longer correct.