Duplicate r value for an address: only an issue for a multi-input Tx?
Any reused nonce is a problem, it's not restricted to a single transaction. 

No competent software will ever reuse nonces accidentally, so using a scanning script like that is just ruining your privacy for no real benefit. Bitcoin Core, Electrum and Armory all use RFC 6979 deterministic nonces so there is no room for RNG failure in these cases, though any software faulty enough to fall at that hurdle will have used the same RNG to make the private keys as well.