There is a multitude of reasons to use one or the other.
Colony counting is often used on petri dishes for antibiotic resistance screening for practical reasons. One of the downside of this versus cell counting is the need to incubate the bacteria for 12h+ after you have done your experiment before having the result.
In some cases, you will need to know the concentration of cells you have immediately to perform specific dilutions or calibrations etc, you then use cell counting.
Cell counting is normally done with a liquid culture of the bacteria. it can be used to determine the concentration of the whole culture or count during or shortly after an experiment. Some bacteria will have a hard time growing on solid media or some molecules that you might want to test for resistance are not soluble, so you can't plate them to colony count.
So it basically all depends on your needs for the specific experiment and what you are working with (bacteria, medium, molecules etc.).