A classic joystick can only control two axes, while a spacecraft operates on six, that's the big problem. Having one work as a "multi-throttle" will give you two axes of translation - say, fore-aft and up-down but not left-right. So you will have to cover left-right with the other stick by rolling like an aeroplane and then yawing, and so you can't do left-right at a standstill, only in forward (or aft) motion. Clumsy in tight spots, such as shuttlebays...
For three axes, you need a z-axis-twisting joystick, i.e. something like those balls. But why not add translation there, too, and do away with the second stick? Twist for angle, push/pull for thrust.
Six? I count three. One of which is not strictly necessary to get around in in three dimensions. If you can pitch and roll, which are already three dimensional maneuvers in a real sense, you can get along fine. Now, I agree that yaw is a pretty useful function.
I remember back in the day playing the old TIE Fighter combat simulator came on my old PC as a teenager... I think I almost never actually made use of the yaw function, and I could maneuver around just fine! It's only occasionally really needed. Pitch and roll can get you around just fine and I figure the "plus sign" shaped "D-pad" (to use the video game parlance) would be all you'd mostly need to get around. I'm sure a simple "shift key" would be all you'd need to make one of the bars be used for yaw. Or even maybe you touch one of the quadrant areas of the circle and pull that around in circles to indicate a yaw motion. I'm sure that would work just fine.