Are there any changes to the way PKI tokens work in version 6.0?
In general, PKI tokens work the same way in version 6.0 as they did in version 5.x. There will be a couple of exceptions that will perform the initialization in the pre-boot environment and not require the certificates to be in Active Directory. Unless the token you are using has this functionality mentioned explicitly, the functionality remains the same as version 5.x.