When you format a card, you're not overwriting all of the data on it. That's why a format is relatively fast.
Otherwise, it would take a very long time (just like trying to fill up a card with images, you'd be limited to the write speed to media). ;-)
A format is simply recreating the FAT (File Allocation Table), and it's unlikely that it's going to make much difference in card life compared to deleting the files.
I haven't had a problem with a card doing it yet (and I've been reformatting my memory cards prior to every use for years using a camera's menus for format).