SU, as far as I know, is the same as actually logging in as root.
The only thing I know that may not work is running scripts that have password-less logins that require root access. (for example some automatic rsync backup scripts are set up this way)
If you simply need a root command prompt on a remote machine, SU works great. It is far safer to disable root logins. The reason is that, one-- they have to guess a valid user name, two -- they have to brute force 2 passwords (the user that they guessed and the root password -- dont let anyone give ya the finger, disable finger).
Have fun and be safe