What other currencies have same malleability vulnerability as Bitcoin? Malleability of Bitcoin protocol has contributed to major losses and represents uncomfortable risk to Bitcoin investors in addition to possibility of 51% attack that depends on promise of biggest mining pool.

Of course, any centralized exchange company can run away with depositors money, but, at least, currency protocol should be strong enough to not allow exchange company owners to blame losses on protocol and hackers.

Do Ethereum or NXT or counterparty or ripple or mint or any in top 10 have same vulnerability ?
This is a quite hard analysis to make. In general all alt-coins that are based on the concept of dynamic input-scripts and output-scripts are subject to transaction malleability. This is because anybody could change the input scripts of a transaction, by adding commands that wouldn't alter the validity of the script, but would alter its hash. For example adding OP_DROP will leave the stack exactly as before prior to scriptPubKey execution.