I don't see how a macro for ninja (assuming the 3 skills combined to create the desired effect can be macroed to an equal or faster time than manually) Can be a bad thing.

The only disadvantage I can imagine is if you have 5 different mudras (I II III IV V VI) and you are going I II III for a certain effect but something happens on the battlefield where you are mid combo and decide to switch to I II IV which could be more effective for example an AOE when a bunch of adds pop like garuda's feathers. That seems to be entirely massively situational and judging at the speed they are used already would require really good timing.

In my opinion I would imagine macroing the mudra's would make perfect sense as you could have all the desired outcomes neatly organised to be used at will, even more so if they can be done with minimal wait times that could be quicker than human input.