While it looks like a good idea at first sight, I would be reluctant to use it. I create backups for cases where files are gone, for whatever reason. One of these reasons might be a cleaner-application (like CCleaner) that accidently removes more files than it should be. If the files that the cleaner is going to remove are automatically excluded from the backup, I have no way to recover form these cleaner mistakes by using my backups.
Of course: if the option configurable then it’s totally up to the user to enable or disable it, but I would use it with caution.