References are unlike regular properties: they are an Authoring-only concept: this is why SetParam does not get called.
Note that plug-ins seldom require references to implement their behavior, and so the plug-in API provides no special facility for them.
Getting the ShortID cannot be done directly through the plug-in API: references are not properties and so cannot be queried through the m_propertySet.
Using a WAAPI query will allow you to retrieve the AkUniqueID. The synchronization with the Authoring for cases when the referenced object is deleted however is harder to achieve (there is no publish-subscribe in the plug-in API at the moment).
Nevertheless, you can save this value to a AK::Wwise::Plugin::CustomData for serialization yes, but it could also be saved into the property set as a uint32 once you have obtained the value from WAAPI.