It all depends. You probably realize that no synth sounds exactly like the other. Don't think "Hardware/Software" just think different synths. Whenever you use one to emulate the other there are always differences in the results. Some people really really care about those differences. Some either don't care or simply don't have the ear to be able to tell the difference.

In other words it is a very individual thing.
Some guys don't mind mouse clicking. Some guys can't stand it and prefer knobs, sliders and even patchchords.

-ED-