After Crash 2.0 corps created GOD to police the Matrix. It took them awhile (bureaucracy amirite), but they eventually created new wireless protocols for the Matrix that restrict what commlinks can do. However, they still need a way to edit files and do things so they created a new device, and just so happen to call them cyberdecks. They aren't anything like the cyberdecks of old, but they do have a lot of specialized hardware that allows them to subvert Matrix protocols. They're also a bit larger than a commlink, think ipad, while commlinks are iphones.
If you want more, Stormfront has some more details on the transition.