So they should make it with every new HD it's a new PC?
No, with every HD it's a new operating system.
So you need a new license then right?
If you keep the old harddrive, then yes. If you're planning on destroying the harddrive, then you can phone Microsoft and alert them to the travesty. But in any case, if you replace the harddrive then you have to re-install Windows anyway, so same key or different it makes sense that your OS stops working.
No matter what you do, if you replace your motherboard, it shouldn't cause your OS, which is firmly attached the harddrive and not at all attached to the motherboard, to stop working.