There really is no point in removing the existing messaging app.
The actual transmission, reception and storage of messages is all handled by the OS itself. Both the default app and handcent merely give you different ways to view and manipulate stored messages (and compose new ones) - if you delete a message in handcent it disappears from the default app too, and vice versa.
You can turn off notifications from the default app by running it and selecting [menu] -> settings -> notifications. Once youve done this, the only impact the default app has on your system is a few kb of storage (hardly a big deal since handcent takes a couple of Mb IIRC). Not really worth the effort of rooting to remove it, and certainly not worth the risk of breaking something else that needs it.