Just like using CLIs does not preclude using a mouse, using GUIs does not preclude using keyboard shortcuts ;)
Quick Explorer example (sometimes I mix and match, maybe I want to show something to a colleague):
explorer . # does what you'd expect; alternatively Win-e
Alt-d # focus path in Explorer
Start typing, Explorer autocompletes stuff
Enter
Tab around, if need be, to change panels
And this is with what is, basically, the dumbest common GUI file manager out there :)
Really depends on the workflow. If I know where I'm navigating then I prefer cd, if I don't then a gui is better than a cd/ls loop. Fortunately programs like ranger cover the latter quite well too.
This is how I do all my file navigation.
This is through cygwin, real linux is another story. I don't know what the difference is between how windows and linux mount remote drives, but the performance difference is stark, ls on a mounted network drive in linux is essentially instant but there is a noticeable lag doing the same from a windows machine.
When you need to open a shell in a certain directory, do you use cd or do you navigate using a GUI? I much prefer the tab-completion I get with the former, especially in hierarchies with high branching factor.