Having done a CS PhD it very much depends on the field. Yeah you'd be laughed at for running an algorithm to find out run time, but areas like information retrieval tends to involve humans and their reactions enough that experimental design is at the forefront, rather than big-o.
CS is more math than science. Running an algorithm to find out its (asymptotic) running time would be laughed at by most CSs,they would go by calculating big-o