cp -R vs Super-duper vs CCC
Yes, there is a difference. In fact, I suspect there are several.

One of the most obvious is that when you delete a file in your Home directory, the cp command won’t know to delete it from the other drives.

Also, cp isn’t smart enough to know if a file has changed or not, so it’s going to copy all of your files each time you run it, which is going to be a huge waste of time for the majority of your data.

Then there are permissions, and special files, and so forth.

So, in short, don’t use cp for this.

rsync would be a much better choice than cp … but, having said that, I should add that I firmly believe there are only 2 kinds of people in the world: 


people who have accidentally deleted data with rsync, and 
people who have never used rsync. 


Which is to say, be careful with rsync, especially when using it to delete files. Start with a small set of files/folders which are either duplicated/backed up somewhere safe or unimportant, and don’t forget to use --dry-run before you run a new rsync command.

Personally, I think CCC or SuperDuper are well worth the money (in fact, I own them both), and would much rather use them than any other method of making a backup.