Yup, Bittrex have already carried out the swap, so the Nautiluscoin on 'Trex is the new NXT MS-based NAUT.

Check through the NAUT redemption thread for more information:
https://bitcointalk.org/index.php?topic=1182317.0

If you want to move your NAUT out of Bittrex....get a NXT client sorted out.