To an experienced user, GUIs tend to be slower because of indirect (eg visual) feedback you need to also react to before the next step is taken.
Take a very analog input element - a rotary switch. For somebody operating this switch or a similarly built one all the time, setting it one step or for example 5 steps is an instant, atomic, single-thought operation that also can be expected to unquestionably have the intended effect. An especially big problem rampant in today's GUIs is how an error condition will require further, and different interaction before the intended input is even finished - so operating a GUI very fast relying on interaction elements always being in a predictable state is error prone.
A GUI tends to need more focus and interaction, in the worst case for 5 cycles in that example - a universal but proportional input method (eg a mouse or trackball) is going to either need sophisticated haptic feedback technology or be very sensitive to overshoot, errors due to environmental vibration... 242
Compare steering wheels, levers ... compare trained users of mechanical cameras, musical instruments or analog-era test equipment...
Also, a GUI becomes extremely confusing to operate if the display is rotated from what you are used to - which can easily happen when gravity is negotiable. If you really want to know, pitch your monitor sideways and try to operate your computer..
As for command line interfaces, not only is usage far more easily documentable (though not as self documenting!) without room for error (as was mentioned already), you can also more easily automate-as-you go by reusing the commands in programs, and it is far easier to remote control such a system on a high-latency, limited bandwith link - character data is very small, and the need for constant interaction is limited.
Also, the materials used for a graphical display might be too hazardous to a given mission in case of damage - CRTs can implode, throw glass shrapnel around, and leave dangerous voltages exposed; big LCDs or similar could be poisonous to crew or corrosive to other materials if whatever leaks stays in the closed-system atmosphere ... 284