This is my understanding; if I'm wrong please let me know.
Your ssh configuration does not affect local users; only users connecting over the open Internet.
I'm betting that DirectAdmin itself doesn't even care if ssh exists on your server. It doesn't know your admin password (it gives you one when it installs, but if you change it, then DirectAdmin doesn't have the new one and DirectAdmin continues to work).
In short it shouldn't affect anything.
Jeff