Your clients will not be affected as long as they produce/consume messages that conform to the abstract contract defined in WSDL.
How difficult the migration is, depends on how much Axis specific API usages you have in your endpoints. Ideally you would have none.
The WS4EE packaging and deployment model is fairly straint forward. Another benefit is of course the usage of standard J2EE web services that are BP-1.0 compliant.
We will at some point in the future drop support for JBoss.NET.