I remove KORD FS9 & FSX via Addon/Remove programme.
The KORD V2 installer will tell you to this so, simply follow what it says.
Install the new updates, is my registration key needed?
As explained many time on the forum, uninstalling/reinstalling will never, ever, affect the registration. Only changing major hardware components or reinstalling Windows from scratch will. Even a complete FSX reinstall will not affect registration, as long as you don't change hardware or reinstall Windows at the same time.
Do I need to uninstall the Addon Manager if prompted, and do I need to un-install any other FSDT files for FS9 or FSX if prompted.
You have to uninstall the Addon Manager only if you don't want to use any FSDT scenery anymore, or for troubleshooting reasons, not normally.
You have to uninstall/reinstall another FSDT scenery only in case you see the "outdated scenery" message. In that case, you have to install it using the current installer, not an old one you already had.
Will all my other FSDT airports be affected, and why is my FS9 KORD still showing and FSX not.
Because you are using an old version of KORD in FSX and haven't followed the message that told you to update.