Duplicate r value for an address: only an issue for a multi-input Tx? I've modified the r-scan Python code to look beyond the 50 Txs the Blockchain.info API usually returns. 

My modifications take all the r values for my address and look for duplicates, but a commented out section of code makes mention of just checking the TxIDs which have more than one input script.

Is it only Txs with multiple inputs that are the problem?
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.