The Nikon will not automatically overwrite your Canon photos. It's not a predator. If you tell it to format the card, obviously it will delete everything on the card, but you don't HAVE to do that - the Nikon will create a new folder for its pictures and work fine. Further, my experience with Canons is that they use IMG_ for the filenames, while Nikon uses DSC_ (by default, but this can be changed on some cameras), so even if it uses the same folders, the filenames shouldn't overlap. And even if they did, the camera should be checking before writing so that it doesn't overwrite a file.
Digital cameras use the same file systems (either FAT32 or exFAT, depending on the size), a card used in a Canon will be readable in a Nikon, and vice versa.
I do agree with formatting when it makes sense, such as after copying everything off the card. Windows and OS X will leave small, hidden "preview" files (and other info) on the card to speed up access, so even if you delete the main pictures, the previews can still be there, taking up space, and over time that starts to add up. So, as other said, I also like to format after copying the pictures to the computer.
I wouldn't store pictures on an SD card for longer than necessary, though. It's easy to forget what's on a card and lose pictures the next time you format, or lose track of what you did and didn't copy off of the card. And SD cards do die from time to time.