In theory, backing up a booted Unix volume is a bad idea because there are a large number of open files all the time on any Unix system, and it's long been considered bad form to attempt to copy an open file. On top of that, a Unix boot volume is unstable; it's constantly being read from and written to even when the computer is just sitting there.
In practice, well-behaved systems limit the file reads and writes, especially with temporary files or VM files, to well-known directories that can be excluded from the backup.
There are times when backing up a booted volume can lead you into trouble. For example, if you use Apple's Mail.app, it keeps incoming messages stored as files on the hard drive, and it indexes the mailboxes using a SQLite database that's always open for writing as long as Mail.app is running. Backing up the mailbox directories or the SQLite database at the moment mail comes in will result in a backup that isn't coherent, is missing some of the files, or both.
I make clones of my booted volumes all the time, but I make a point to ensure that no user-level applications are running when I do it.
