Probably a good point, but I imagine he would piss Nova off; he would likely hassle her until she joined his army.
She wouldn't join his army, she doesn't take orders well, she'd probably end up setting off explosions on him to make him leave her alone. Yeah he'd piss her the hell off.
Eh, Ganondorf would likely be an interesting fight for Nova. He wouldn't likely be hurt (SCP has not discovered this yet) but only Link's arrows in certain forms (Light) were able to hurt him very much.