Just to add to Alan's answer - one of the nice things about WMQ AMS is that the administrator defines policies that get applied to individual queues, not to the whole queue manager. This means that you can identify the routes through your WMQ network which need to be protected and encrypted and apply security policies on an appropriate basis. So you could transparently cause only those messages and queues containing customer payment details (for example), but leave SSL channels and standard MQ security to cover the other security requirements for the rest of your message data.
The key points here are to be pragmatic, and apply the right levels of security in the right places. There will be a balance between performance, the needs of your application and your business, and the technology. Try it and see what is most appropriate.