walletnotify and transaction malleability
Yes. You receieve a walletnotify for every transaction your wallet sees that is relevant to it. Once when it is first seen, and once when it is seen in a block (first confirmation). These two may coincide, in which case you only get the confirmation one.

For mutated transactions, you will see a first one that never confirms (and in 0.9 will get a "-1" confirmations marker), and a second transaction that does confirm.