the camera will generally specify the appropriate cluster size. also, some older cameras are very finicky about formatting. formatting in camera is quick and ensures that new data isn't written to the same set of NAND cells every time. using the computer to 'delete' images doesn't. with today's flash memory, it really doesn't matter but older CF (like in the days of 32 meg cards) it was very common to 'wear out' cards as they were often only rated for 5,000 cycles. today's memory card cells are rated in excess of 100,000 cycles and the onboard controllers automatically map bad cells. sure you may find that after 100,000 pictures, your card may have decreased capacity, but not by very much - because formatting ensures random cell usage.
btw i always format in-camera. it's just 3 clicks through the menu.