From the card's perspective, there really isn't any difference between what the camera does while formatting and when it's writing pictures. It's all just data written to blocks on the device* and you're not doing it any harm.

The format done by a camera does a couple of small writes: a fresh partition table and new file system headers. Both of these make the volume look like there's nothing on it. You're actually doing the cards a favor longevity-wise, because this doesn't wear the flash as much as the writes it would take to remove the files individually or to write zeros to every block. This is a very small favor in the grand scheme of things because thousands of blocks are written each time you take a picture.

*The command set used by most memory cards includes a "format" command that tells the device to prepare itself for use. This is a holdover from the days when magnetic disks came out of the factory unformatted, and what it does is vendor- and product-specifc. On memory cards it should do nothing.